sending incremental file list
./
16S/Rexport/
RNAseq/
RNAseq/README.txt
RNAseq/2018_EA_subging_gingivitis/
RNAseq/2018_EA_subging_gingivitis/cmat_ko.txt
RNAseq/2018_EA_subging_gingivitis/cmatr.gff
RNAseq/2018_EA_subging_gingivitis/condition1_cmatmonorich_counts1.txt
RNAseq/2018_EA_subging_gingivitis/condition1_cmatmonorich_counts2.txt
RNAseq/2018_EA_subging_gingivitis/condition2_submeta_counts1.txt
RNAseq/2018_EA_subging_gingivitis/condition2_submeta_counts2.txt
RNAseq/2018_EA_subging_gingivitis/condition2_submeta_counts3.txt
RNAseq/2018_EA_subging_gingivitis/deseq_tablesandkegg.R
RNAseq/2018_EA_subging_gingivitis/may2020_kegg.csv
RNAseq/2018_EA_subging_gingivitis/script1.sh
RNAseq/2018_EA_subging_gingivitis/script2.sh
RNAseq/2018_EA_subging_gingivitis/slurm-1672003.out
RNAseq/2018_EA_subging_gingivitis/slurm-1672004.out
RNAseq/2018_EA_subging_gingivitis/slurm-1672008.out
RNAseq/2018_EA_subging_gingivitis/slurm-1672009.out
RNAseq/2018_EA_subging_gingivitis/standaloneR.sh
RNAseq/2018_EA_subging_gingivitis/figures/
RNAseq/2018_EA_subging_gingivitis/figures/overexpressed_highest_category.svg
RNAseq/2018_EA_subging_gingivitis/figures/overexpressed_lowest_category.svg
RNAseq/2018_EA_subging_gingivitis/figures/pcaplot.svg
RNAseq/2018_EA_subging_gingivitis/figures/repressed_highest_category.svg
RNAseq/2018_EA_subging_gingivitis/figures/repressed_lowest_category.svg
RNAseq/2018_EA_subging_gingivitis/figures/volcanoplot.svg
RNAseq/2018_EA_subging_gingivitis/kegg_analysis/
RNAseq/2018_EA_subging_gingivitis/kegg_analysis/allsig_condition2_vs_condition1_kegg.csv
RNAseq/2018_EA_subging_gingivitis/kegg_analysis/downsig_condition2_vs_condition1_kegg.csv
RNAseq/2018_EA_subging_gingivitis/kegg_analysis/overexpressed_kegg_summary_cathigh.csv
RNAseq/2018_EA_subging_gingivitis/kegg_analysis/overexpressed_kegg_summary_catlow.csv
RNAseq/2018_EA_subging_gingivitis/kegg_analysis/raw_kegg_table.csv
RNAseq/2018_EA_subging_gingivitis/kegg_analysis/repressed_kegg_summary_cathigh.csv
RNAseq/2018_EA_subging_gingivitis/kegg_analysis/repressed_kegg_summary_catlow.csv
RNAseq/2018_EA_subging_gingivitis/kegg_analysis/upsig_condition2_vs_condition1_kegg.csv
RNAseq/2018_EA_subging_gingivitis/rnaseq_analysis/
RNAseq/2018_EA_subging_gingivitis/rnaseq_analysis/allsig_conditon2_vs_condition1.csv
RNAseq/2018_EA_subging_gingivitis/rnaseq_analysis/downsig_conditon2_vs_condition1.csv
RNAseq/2018_EA_subging_gingivitis/rnaseq_analysis/raw_condition2_vs_condition1.csv
RNAseq/2018_EA_subging_gingivitis/rnaseq_analysis/raw_deseqtable.csv
RNAseq/2018_EA_subging_gingivitis/rnaseq_analysis/upsig_conditon2_vs_condition1.csv
RNAseq/2020_transcriptome_analyses_AL/
RNAseq/2020_transcriptome_analyses_AL/2023_kegg_ko.csv
RNAseq/2020_transcriptome_analyses_AL/Data/
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/condition1_smitimonoaero_counts1.txt
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/condition1_smitimonoaero_counts2.txt
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/condition2_cmatr_smiti_aero_counts1.txt
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/condition2_cmatr_smiti_aero_counts2.txt
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/slurm-1652683.out
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/slurm-1663627.out
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/slurm-1663629.out
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/slurm-1663631.out
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/slurm-1663634.out
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/slurm-1663684.out
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/figures/
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/figures/overexpressed_highest_category.svg
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/figures/overexpressed_lowest_category.svg
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/figures/pcaplot.svg
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/figures/repressed_highest_category.svg
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/figures/repressed_lowest_category.svg
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/figures/volcanoplot.svg
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/kegg_analysis/
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/kegg_analysis/allsig_condition2_vs_condition1_kegg.csv
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/kegg_analysis/downsig_condition2_vs_condition1_kegg.csv
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/kegg_analysis/overexpressed_kegg_summary_cathigh.csv
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/kegg_analysis/overexpressed_kegg_summary_catlow.csv
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/kegg_analysis/raw_kegg_table.csv
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/kegg_analysis/repressed_kegg_summary_cathigh.csv
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/kegg_analysis/repressed_kegg_summary_catlow.csv
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/kegg_analysis/upsig_condition2_vs_condition1_kegg.csv
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/rnaseq_analysis/
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/rnaseq_analysis/allsig_conditon2_vs_condition1.csv
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/rnaseq_analysis/downsig_conditon2_vs_condition1.csv
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/rnaseq_analysis/raw_condition2_vs_condition1.csv
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/rnaseq_analysis/raw_deseqtable.csv
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/rnaseq_analysis/upsig_conditon2_vs_condition1.csv
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/condition1_smitimonoana_counts1.txt
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/condition1_smitimonoana_counts2.txt
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/condition2_cmatr_smiti_ana_counts1.txt
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/condition2_cmatr_smiti_ana_counts2.txt
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/slurm-1652684.out
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/slurm-1652898.out
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/figures/
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/figures/overexpressed_highest_category.svg
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/figures/overexpressed_lowest_category.svg
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/figures/pcaplot.svg
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/figures/repressed_highest_category.svg
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/figures/repressed_lowest_category.svg
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/figures/volcanoplot.svg
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/kegg_analysis/
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/kegg_analysis/allsig_condition2_vs_condition1_kegg.csv
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/kegg_analysis/downsig_condition2_vs_condition1_kegg.csv
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/kegg_analysis/overexpressed_kegg_summary_cathigh.csv
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/kegg_analysis/overexpressed_kegg_summary_catlow.csv
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/kegg_analysis/raw_kegg_table.csv
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/kegg_analysis/repressed_kegg_summary_cathigh.csv
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/kegg_analysis/repressed_kegg_summary_catlow.csv
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/kegg_analysis/upsig_condition2_vs_condition1_kegg.csv
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/rnaseq_analysis/
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/rnaseq_analysis/allsig_conditon2_vs_condition1.csv
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/rnaseq_analysis/downsig_conditon2_vs_condition1.csv
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/rnaseq_analysis/raw_condition2_vs_condition1.csv
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/rnaseq_analysis/raw_deseqtable.csv
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/rnaseq_analysis/upsig_conditon2_vs_condition1.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/slurm-1767857.out
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/figures/
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/figures/condition1_smitimonoaero_counts1.txt
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/figures/condition1_smitimonoaero_counts2.txt
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/figures/condition2_submeta_counts1.txt
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/figures/condition2_submeta_counts2.txt
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/figures/condition2_submeta_counts3.txt
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/figures/overexpressed_highest_category.svg
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/figures/overexpressed_lowest_category.svg
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/figures/pcaplot.svg
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/figures/repressed_highest_category.svg
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/figures/repressed_lowest_category.svg
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/figures/slurm-1767856.out
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/figures/volcanoplot.svg
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/kegg_analysis/
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/kegg_analysis/allsig_condition2_vs_condition1_kegg.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/kegg_analysis/downsig_condition2_vs_condition1_kegg.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/kegg_analysis/overexpressed_kegg_summary_cathigh.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/kegg_analysis/overexpressed_kegg_summary_catlow.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/kegg_analysis/raw_kegg_table.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/kegg_analysis/repressed_kegg_summary_cathigh.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/kegg_analysis/repressed_kegg_summary_catlow.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/kegg_analysis/upsig_condition2_vs_condition1_kegg.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/rnaseq_analysis/
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/rnaseq_analysis/allsig_conditon2_vs_condition1.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/rnaseq_analysis/downsig_conditon2_vs_condition1.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/rnaseq_analysis/raw_condition2_vs_condition1.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/rnaseq_analysis/raw_deseqtable.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/rnaseq_analysis/upsig_conditon2_vs_condition1.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/condition2_smhp_ana_counts1.txt
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/condition2_smhp_ana_counts2.txt
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/slurm-1766020.out
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/figures/
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/figures/overexpressed_highest_category.svg
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/figures/overexpressed_lowest_category.svg
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/figures/pcaplot.svg
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/figures/repressed_highest_category.svg
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/figures/repressed_lowest_category.svg
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/figures/volcanoplot.svg
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/kegg_analysis/
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/kegg_analysis/allsig_condition2_vs_condition1_kegg.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/kegg_analysis/downsig_condition2_vs_condition1_kegg.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/kegg_analysis/overexpressed_kegg_summary_cathigh.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/kegg_analysis/overexpressed_kegg_summary_catlow.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/kegg_analysis/raw_kegg_table.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/kegg_analysis/repressed_kegg_summary_cathigh.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/kegg_analysis/repressed_kegg_summary_catlow.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/kegg_analysis/upsig_condition2_vs_condition1_kegg.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/rnaseq_analysis/
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/rnaseq_analysis/allsig_conditon2_vs_condition1.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/rnaseq_analysis/downsig_conditon2_vs_condition1.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/rnaseq_analysis/raw_condition2_vs_condition1.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/rnaseq_analysis/raw_deseqtable.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/rnaseq_analysis/upsig_conditon2_vs_condition1.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/condition1_smitimonoana_counts1.txt
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/condition1_smitimonoana_counts2.txt
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/condition2_submeta_counts1.txt
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/condition2_submeta_counts2.txt
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/condition2_submeta_counts3.txt
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/slurm-1766021.out
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/slurm-1766023.out
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/figures/
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/figures/overexpressed_highest_category.svg
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/figures/overexpressed_lowest_category.svg
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/figures/pcaplot.svg
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/figures/repressed_highest_category.svg
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/figures/repressed_lowest_category.svg
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/figures/volcanoplot.svg
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/kegg_analysis/
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/kegg_analysis/allsig_condition2_vs_condition1_kegg.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/kegg_analysis/downsig_condition2_vs_condition1_kegg.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/kegg_analysis/overexpressed_kegg_summary_cathigh.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/kegg_analysis/overexpressed_kegg_summary_catlow.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/kegg_analysis/raw_kegg_table.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/kegg_analysis/repressed_kegg_summary_cathigh.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/kegg_analysis/repressed_kegg_summary_catlow.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/kegg_analysis/upsig_condition2_vs_condition1_kegg.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/rnaseq_analysis/
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/rnaseq_analysis/allsig_conditon2_vs_condition1.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/rnaseq_analysis/downsig_conditon2_vs_condition1.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/rnaseq_analysis/raw_condition2_vs_condition1.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/rnaseq_analysis/raw_deseqtable.csv
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/rnaseq_analysis/upsig_conditon2_vs_condition1.csv
RNAseq/2020_transcriptome_analyses_AL/FastQ/
RNAseq/2020_transcriptome_analyses_AL/FastQ/atcc_hpara.fna
RNAseq/2020_transcriptome_analyses_AL/FastQ/hpara.fasta
RNAseq/2020_transcriptome_analyses_AL/Sm_mono_aero_vs_ana/
RNAseq/2020_transcriptome_analyses_AL/Sm_mono_aero_vs_ana/slurm-1769139.out
RNAseq/2020_transcriptome_analyses_AL/Sm_mono_aero_vs_ana/figures/
RNAseq/2020_transcriptome_analyses_AL/Sm_mono_aero_vs_ana/figures/overexpressed_highest_category.svg
RNAseq/2020_transcriptome_analyses_AL/Sm_mono_aero_vs_ana/figures/overexpressed_lowest_category.svg
RNAseq/2020_transcriptome_analyses_AL/Sm_mono_aero_vs_ana/figures/pcaplot.svg
RNAseq/2020_transcriptome_analyses_AL/Sm_mono_aero_vs_ana/figures/repressed_highest_category.svg
RNAseq/2020_transcriptome_analyses_AL/Sm_mono_aero_vs_ana/figures/repressed_lowest_category.svg
RNAseq/2020_transcriptome_analyses_AL/Sm_mono_aero_vs_ana/figures/volcanoplot.svg
RNAseq/2020_transcriptome_analyses_AL/Sm_mono_aero_vs_ana/kegg_analysis/
RNAseq/2020_transcriptome_analyses_AL/Sm_mono_aero_vs_ana/kegg_analysis/allsig_condition2_vs_condition1_kegg.csv
RNAseq/2020_transcriptome_analyses_AL/Sm_mono_aero_vs_ana/kegg_analysis/downsig_condition2_vs_condition1_kegg.csv
RNAseq/2020_transcriptome_analyses_AL/Sm_mono_aero_vs_ana/kegg_analysis/overexpressed_kegg_summary_cathigh.csv
RNAseq/2020_transcriptome_analyses_AL/Sm_mono_aero_vs_ana/kegg_analysis/overexpressed_kegg_summary_catlow.csv
RNAseq/2020_transcriptome_analyses_AL/Sm_mono_aero_vs_ana/kegg_analysis/raw_kegg_table.csv
RNAseq/2020_transcriptome_analyses_AL/Sm_mono_aero_vs_ana/kegg_analysis/repressed_kegg_summary_cathigh.csv
RNAseq/2020_transcriptome_analyses_AL/Sm_mono_aero_vs_ana/kegg_analysis/repressed_kegg_summary_catlow.csv
RNAseq/2020_transcriptome_analyses_AL/Sm_mono_aero_vs_ana/kegg_analysis/upsig_condition2_vs_condition1_kegg.csv
RNAseq/2020_transcriptome_analyses_AL/Sm_mono_aero_vs_ana/rnaseq_analysis/
RNAseq/2020_transcriptome_analyses_AL/Sm_mono_aero_vs_ana/rnaseq_analysis/allsig_conditon2_vs_condition1.csv
RNAseq/2020_transcriptome_analyses_AL/Sm_mono_aero_vs_ana/rnaseq_analysis/downsig_conditon2_vs_condition1.csv
RNAseq/2020_transcriptome_analyses_AL/Sm_mono_aero_vs_ana/rnaseq_analysis/raw_condition2_vs_condition1.csv
RNAseq/2020_transcriptome_analyses_AL/Sm_mono_aero_vs_ana/rnaseq_analysis/raw_deseqtable.csv
RNAseq/2020_transcriptome_analyses_AL/Sm_mono_aero_vs_ana/rnaseq_analysis/upsig_conditon2_vs_condition1.csv
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/condition2_submeta_counts1.txt
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/condition2_submeta_counts2.txt
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/condition2_submeta_counts3.txt
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/figures/
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/figures/overexpressed_highest_category.svg
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/figures/overexpressed_lowest_category.svg
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/figures/pcaplot.svg
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/figures/repressed_highest_category.svg
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/figures/repressed_lowest_category.svg
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/figures/volcanoplot.svg
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/kegg_analysis/
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/kegg_analysis/allsig_condition2_vs_condition1_kegg.csv
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/kegg_analysis/downsig_condition2_vs_condition1_kegg.csv
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/kegg_analysis/overexpressed_kegg_summary_cathigh.csv
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/kegg_analysis/overexpressed_kegg_summary_catlow.csv
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/kegg_analysis/raw_kegg_table.csv
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/kegg_analysis/repressed_kegg_summary_cathigh.csv
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/kegg_analysis/repressed_kegg_summary_catlow.csv
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/kegg_analysis/upsig_condition2_vs_condition1_kegg.csv
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/rnaseq_analysis/
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/rnaseq_analysis/allsig_conditon2_vs_condition1.csv
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/rnaseq_analysis/downsig_conditon2_vs_condition1.csv
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/rnaseq_analysis/raw_condition2_vs_condition1.csv
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/rnaseq_analysis/raw_deseqtable.csv
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/rnaseq_analysis/upsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/
RNAseq/2023_AL_RNAseq/2023_CM_AL/
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/bowtie_build.sh
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/cmat_ko.txt
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/cmatr.gff
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/condition1_cmatrmonoaero_counts1.txt
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/condition1_cmatrmonoaero_counts2.txt
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/condition2_cmatr_scris_aero_counts1.txt
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/condition2_cmatr_scris_aero_counts2.txt
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/deseq_tablesandkegg.R
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/may2020_kegg.csv
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/paired_end_duplicate_analysis.sh
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/slurm-2038759.out
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/slurm-2038760.out
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/slurm-2038761.out
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/slurm-2038763.out
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/standaloneR.sh
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/figures/
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/figures/overexpressed_highest_category.svg
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/figures/overexpressed_lowest_category.svg
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/figures/pcaplot.svg
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/figures/repressed_highest_category.svg
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/figures/repressed_lowest_category.svg
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/figures/volcanoplot.svg
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/kegg_analysis/
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/kegg_analysis/allsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/kegg_analysis/downsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/kegg_analysis/overexpressed_kegg_summary_cathigh.csv
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/kegg_analysis/overexpressed_kegg_summary_catlow.csv
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/kegg_analysis/raw_kegg_table.csv
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/kegg_analysis/repressed_kegg_summary_cathigh.csv
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/kegg_analysis/repressed_kegg_summary_catlow.csv
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/kegg_analysis/upsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/rnaseq_analysis/
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/rnaseq_analysis/allsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/rnaseq_analysis/downsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/rnaseq_analysis/raw_condition2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/rnaseq_analysis/raw_deseqtable.csv
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/rnaseq_analysis/upsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/bowtie_build.sh
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/cmatr.gff
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/cmatr_ko.txt
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/condition1_cmatrmonoaero_counts1.txt
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/condition1_cmatrmonoaero_counts2.txt
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/condition2_cmatr_smiti_aero_counts1.txt
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/condition2_cmatr_smiti_aero_counts2.txt
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/deseq_tablesandkegg.R
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/may2020_kegg.csv
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/paired_end_duplicate_analysis.sh
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/slurm-2038765.out
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/standaloneR.sh
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/figures/
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/figures/overexpressed_highest_category.svg
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/figures/overexpressed_lowest_category.svg
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/figures/pcaplot.svg
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/figures/repressed_highest_category.svg
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/figures/repressed_lowest_category.svg
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/figures/volcanoplot.svg
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/kegg_analysis/
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/kegg_analysis/allsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/kegg_analysis/downsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/kegg_analysis/overexpressed_kegg_summary_cathigh.csv
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/kegg_analysis/overexpressed_kegg_summary_catlow.csv
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/kegg_analysis/raw_kegg_table.csv
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/kegg_analysis/repressed_kegg_summary_cathigh.csv
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/kegg_analysis/repressed_kegg_summary_catlow.csv
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/kegg_analysis/upsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/rnaseq_analysis/
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/rnaseq_analysis/allsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/rnaseq_analysis/downsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/rnaseq_analysis/raw_condition2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/rnaseq_analysis/raw_deseqtable.csv
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/rnaseq_analysis/upsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/condition1_hp_counts1.txt
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/condition1_hp_counts2.txt
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/condition2_hpan_counts1.txt
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/condition2_hpan_counts2.txt
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/deseq_tablesandkegg.R
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/hp_ko.txt
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/hpara.gff
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/may2020_parsed_kegg.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/slurm-2038762.out
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/standaloneR.sh
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/figures/
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/figures/overexpressed_highest_category.svg
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/figures/overexpressed_lowest_category.svg
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/figures/pcaplot.svg
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/figures/repressed_highest_category.svg
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/figures/repressed_lowest_category.svg
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/figures/volcanoplot.svg
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/kegg_analysis/
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/kegg_analysis/allsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/kegg_analysis/downsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/kegg_analysis/overexpressed_kegg_summary_cathigh.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/kegg_analysis/overexpressed_kegg_summary_catlow.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/kegg_analysis/raw_kegg_table.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/kegg_analysis/repressed_kegg_summary_cathigh.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/kegg_analysis/repressed_kegg_summary_catlow.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/kegg_analysis/upsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/rnaseq_analysis/
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/rnaseq_analysis/allsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/rnaseq_analysis/downsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/rnaseq_analysis/raw_condition2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/rnaseq_analysis/raw_deseqtable.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/rnaseq_analysis/upsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/condition1_hpmonoaero_counts1.txt
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/condition1_hpmonoaero_counts2.txt
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/condition2_HPSM_counts1.txt
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/condition2_HPSM_counts2.txt
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/hp_ko.txt
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/hpara.gff
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/slurm-2038724.out
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/figures/
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/figures/overexpressed_highest_category.svg
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/figures/overexpressed_lowest_category.svg
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/figures/pcaplot.svg
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/figures/repressed_highest_category.svg
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/figures/repressed_lowest_category.svg
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/figures/volcanoplot.svg
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/kegg_analysis/
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/kegg_analysis/allsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/kegg_analysis/downsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/kegg_analysis/overexpressed_kegg_summary_cathigh.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/kegg_analysis/overexpressed_kegg_summary_catlow.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/kegg_analysis/raw_kegg_table.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/kegg_analysis/repressed_kegg_summary_cathigh.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/kegg_analysis/repressed_kegg_summary_catlow.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/kegg_analysis/upsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/rnaseq_analysis/
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/rnaseq_analysis/allsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/rnaseq_analysis/downsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/rnaseq_analysis/raw_condition2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/rnaseq_analysis/raw_deseqtable.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/rnaseq_analysis/upsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/condition1_hpmonoana_counts1.txt
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/condition1_hpmonoana_counts2.txt
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/condition2_HPSMANA_counts1.txt
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/condition2_HPSMANA_counts2.txt
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/deseq_tablesandkegg.R
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/hp_ko.txt
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/hpara.gff
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/may2020_kegg.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/paired_end_duplicate_analysis.sh
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/slurm-2038728.out
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/standaloneR.sh
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/figures/
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/figures/overexpressed_highest_category.svg
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/figures/overexpressed_lowest_category.svg
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/figures/pcaplot.svg
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/figures/repressed_highest_category.svg
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/figures/repressed_lowest_category.svg
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/figures/volcanoplot.svg
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/kegg_analysis/
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/kegg_analysis/allsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/kegg_analysis/downsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/kegg_analysis/overexpressed_kegg_summary_cathigh.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/kegg_analysis/overexpressed_kegg_summary_catlow.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/kegg_analysis/raw_kegg_table.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/kegg_analysis/repressed_kegg_summary_cathigh.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/kegg_analysis/repressed_kegg_summary_catlow.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/kegg_analysis/upsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/rnaseq_analysis/
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/rnaseq_analysis/allsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/rnaseq_analysis/downsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/rnaseq_analysis/raw_condition2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/rnaseq_analysis/raw_deseqtable.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/rnaseq_analysis/upsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_HP_AL/hpara/
RNAseq/2023_AL_RNAseq/2023_HP_AL/hpara/desktop.ini
RNAseq/2023_AL_RNAseq/2023_HP_AL/hpara/hpara.1.bt2
RNAseq/2023_AL_RNAseq/2023_HP_AL/hpara/hpara.2.bt2
RNAseq/2023_AL_RNAseq/2023_HP_AL/hpara/hpara.3.bt2
RNAseq/2023_AL_RNAseq/2023_HP_AL/hpara/hpara.4.bt2
RNAseq/2023_AL_RNAseq/2023_HP_AL/hpara/hpara.fasta
RNAseq/2023_AL_RNAseq/2023_HP_AL/hpara/hpara.rev.1.bt2
RNAseq/2023_AL_RNAseq/2023_HP_AL/hpara/hpara.rev.2.bt2
RNAseq/2023_AL_RNAseq/2023_SM_AL/
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMaero/
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMaero/condition1_smitimonoaero_counts1.txt
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMaero/condition1_smitimonoaero_counts2.txt
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMaero/condition2_HPSM_counts1.txt
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMaero/condition2_HPSM_counts2.txt
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMaero/figures/
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMaero/figures/overexpressed_highest_category.svg
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMaero/figures/overexpressed_lowest_category.svg
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMaero/figures/pcaplot.svg
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMaero/figures/repressed_lowest_category.svg
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMaero/figures/volcanoplot.svg
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMaero/kegg_analysis/
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMaero/kegg_analysis/allsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMaero/kegg_analysis/downsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMaero/kegg_analysis/raw_kegg_table.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMaero/kegg_analysis/upsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMaero/rnaseq_analysis/
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMaero/rnaseq_analysis/allsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMaero/rnaseq_analysis/downsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMaero/rnaseq_analysis/raw_condition2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMaero/rnaseq_analysis/raw_deseqtable.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMaero/rnaseq_analysis/upsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/condition1_smitimonoana_counts1.txt
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/condition1_smitimonoana_counts2.txt
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/condition2_HPSMANA_counts1.txt
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/condition2_HPSMANA_counts2.txt
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/deseq_tablesandkegg.R
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/may2020_kegg.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/paired_end_duplicate_analysis.sh
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/slurm-2038726.out
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/slurm-2038727.out
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/smitis.gff
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/smitis_ko.txt
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/standaloneR.sh
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/figures/
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/figures/overexpressed_highest_category.svg
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/figures/overexpressed_lowest_category.svg
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/figures/pcaplot.svg
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/figures/repressed_highest_category.svg
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/figures/repressed_lowest_category.svg
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/figures/volcanoplot.svg
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/kegg_analysis/
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/kegg_analysis/allsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/kegg_analysis/downsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/kegg_analysis/overexpressed_kegg_summary_cathigh.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/kegg_analysis/overexpressed_kegg_summary_catlow.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/kegg_analysis/raw_kegg_table.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/kegg_analysis/repressed_kegg_summary_cathigh.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/kegg_analysis/repressed_kegg_summary_catlow.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/kegg_analysis/upsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/rnaseq_analysis/
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/rnaseq_analysis/allsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/rnaseq_analysis/downsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/rnaseq_analysis/raw_condition2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/rnaseq_analysis/raw_deseqtable.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/rnaseq_analysis/upsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis/
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis/smiti.fa
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis/smitis.1.bt2
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis/smitis.2.bt2
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis/smitis.3.bt2
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis/smitis.4.bt2
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis/smitis.rev.1.bt2
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis/smitis.rev.2.bt2
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/condition1_smitimonoaero_counts1.txt
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/condition1_smitimonoaero_counts2.txt
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/condition2_smiticocultaero_counts1.txt
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/condition2_smiticocultaero_counts2.txt
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/deseq_tablesandkegg.R
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/may2020_kegg.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/slurm-2038721.out
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/smitis.gff
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/smitis_ko.txt
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/standaloneR.sh
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/figures/
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/figures/overexpressed_highest_category.svg
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/figures/overexpressed_lowest_category.svg
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/figures/pcaplot.svg
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/figures/repressed_highest_category.svg
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/figures/repressed_lowest_category.svg
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/figures/volcanoplot.svg
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/kegg_analysis/
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/kegg_analysis/allsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/kegg_analysis/downsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/kegg_analysis/overexpressed_kegg_summary_cathigh.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/kegg_analysis/overexpressed_kegg_summary_catlow.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/kegg_analysis/raw_kegg_table.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/kegg_analysis/repressed_kegg_summary_cathigh.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/kegg_analysis/repressed_kegg_summary_catlow.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/kegg_analysis/upsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/rnaseq_analysis/
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/rnaseq_analysis/allsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/rnaseq_analysis/downsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/rnaseq_analysis/raw_condition2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/rnaseq_analysis/raw_deseqtable.csv
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/rnaseq_analysis/upsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/condition1_smitimonoaero_counts1.txt
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/condition1_smitimonoaero_counts2.txt
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/condition2_MT48_counts1.txt
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/condition2_MT48_counts2.txt
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/condition2_MT48_counts3.txt
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/condition2_MT48_counts4.txt
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/may2020_kegg.csv
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/slurm-2039192.out
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/slurm-2039193.out
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/slurm-2039194.out
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/smitis.gff
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/smitis_ko.txt
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/figures/
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/figures/overexpressed_highest_category.svg
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/figures/overexpressed_lowest_category.svg
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/figures/pcaplot.svg
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/figures/repressed_highest_category.svg
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/figures/repressed_lowest_category.svg
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/figures/volcanoplot.svg
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/kegg_analysis/
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/kegg_analysis/allsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/kegg_analysis/downsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/kegg_analysis/overexpressed_kegg_summary_cathigh.csv
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/kegg_analysis/overexpressed_kegg_summary_catlow.csv
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/kegg_analysis/raw_kegg_table.csv
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/kegg_analysis/repressed_kegg_summary_cathigh.csv
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/kegg_analysis/repressed_kegg_summary_catlow.csv
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/kegg_analysis/upsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/newindex/
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/newindex/smitis.1.bt2
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/newindex/smitis.2.bt2
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/newindex/smitis.3.bt2
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/newindex/smitis.4.bt2
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/newindex/smitis.rev.1.bt2
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/newindex/smitis.rev.2.bt2
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/rnaseq_analysis/
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/rnaseq_analysis/allsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/rnaseq_analysis/downsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/rnaseq_analysis/raw_condition2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/rnaseq_analysis/raw_deseqtable.csv
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/rnaseq_analysis/upsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/condition1_smitimonoaero_counts1.txt
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/condition1_smitimonoaero_counts2.txt
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/condition2_JMT_counts4.txt
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/condition2_JMT_counts5.txt
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/condition2_JMT_counts6.txt
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/condition2_JMT_counts7.txt
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/condition2_JMT_counts8.txt
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/deseq_tablesandkegg.R
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/may2020_kegg.csv
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/piaz.sh
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/slurm-2039202.out
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/slurm-288990.out
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/slurm-288991.out
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/slurm-288992.out
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/smitis.gff
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/smitis_jorth.sh
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/smitis_ko.txt
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/standaloneR.sh
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/figures/
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/figures/overexpressed_highest_category.svg
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/figures/overexpressed_lowest_category.svg
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/figures/pcaplot.svg
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/figures/repressed_highest_category.svg
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/figures/repressed_lowest_category.svg
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/figures/volcanoplot.svg
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/kegg_analysis/
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/kegg_analysis/allsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/kegg_analysis/downsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/kegg_analysis/overexpressed_kegg_summary_cathigh.csv
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/kegg_analysis/overexpressed_kegg_summary_catlow.csv
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/kegg_analysis/raw_kegg_table.csv
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/kegg_analysis/repressed_kegg_summary_cathigh.csv
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/kegg_analysis/repressed_kegg_summary_catlow.csv
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/kegg_analysis/upsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/newindex/
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/newindex/smitis.1.bt2
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/newindex/smitis.2.bt2
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/newindex/smitis.3.bt2
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/newindex/smitis.4.bt2
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/newindex/smitis.rev.1.bt2
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/newindex/smitis.rev.2.bt2
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/rnaseq_analysis/
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/rnaseq_analysis/allsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/rnaseq_analysis/downsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/rnaseq_analysis/raw_condition2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/rnaseq_analysis/raw_deseqtable.csv
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/rnaseq_analysis/upsig_conditon2_vs_condition1.csv
RNAseq/2023_AL_RNAseq/Script testing/
RNAseq/2023_AL_RNAseq/Script testing/2023_kegg.csv
RNAseq/2023_AL_RNAseq/Script testing/condition1_HP_counts1.txt
RNAseq/2023_AL_RNAseq/Script testing/condition1_HP_counts2.txt
RNAseq/2023_AL_RNAseq/Script testing/condition2_HPSM_counts1.txt
RNAseq/2023_AL_RNAseq/Script testing/condition2_HPSM_counts2.txt
RNAseq/2023_AL_RNAseq/Script testing/deseq.sh
RNAseq/2023_AL_RNAseq/Script testing/deseq_tablesandkegg.R
RNAseq/2023_AL_RNAseq/Script testing/deseq_tablesandkegg2.R
RNAseq/2023_AL_RNAseq/Script testing/hpara.gff
RNAseq/2023_AL_RNAseq/Script testing/hpara_ko.txt
RNAseq/2023_AL_RNAseq/Script testing/paired_end_dup.sh
RNAseq/2023_AL_RNAseq/Script testing/paired_end_duplicate_analysis.sh
RNAseq/2023_AL_RNAseq/Script testing/paired_end_test.sh
RNAseq/2023_AL_RNAseq/Script testing/slurm-2038609.out
RNAseq/2023_AL_RNAseq/Script testing/slurm-2038610.out
RNAseq/2023_AL_RNAseq/Script testing/slurm-2038611.out
RNAseq/2023_AL_RNAseq/Script testing/slurm-2038612.out
RNAseq/2023_AL_RNAseq/Script testing/slurm-2038613.out
RNAseq/2023_AL_RNAseq/Script testing/slurm-2038614.out
RNAseq/2023_AL_RNAseq/Script testing/slurm-2038615.out
RNAseq/2023_AL_RNAseq/Script testing/slurm-2038616.out
RNAseq/2023_AL_RNAseq/Script testing/slurm-2038617.out
RNAseq/2023_AL_RNAseq/Script testing/slurm-2038618.out
RNAseq/2023_AL_RNAseq/Script testing/slurm-2038619.out
RNAseq/2023_AL_RNAseq/Script testing/slurm-2038620.out
RNAseq/2023_AL_RNAseq/Script testing/slurm-2038621.out
RNAseq/2023_AL_RNAseq/Script testing/slurm-2038622.out
RNAseq/2023_AL_RNAseq/Script testing/slurm-2038623.out
RNAseq/2023_AL_RNAseq/Script testing/slurm-2038624.out
RNAseq/2023_AL_RNAseq/Script testing/slurm-2038625.out
RNAseq/2023_AL_RNAseq/Script testing/slurm-2038626.out
RNAseq/2023_AL_RNAseq/Script testing/slurm-2038627.out
RNAseq/2023_AL_RNAseq/Script testing/slurm-2038628.out
RNAseq/2023_AL_RNAseq/Script testing/slurm-2038629.out
RNAseq/2023_AL_RNAseq/Script testing/slurm-2038685.out
RNAseq/2023_AL_RNAseq/Script testing/slurm-2038689.out
RNAseq/2023_AL_RNAseq/Script testing/slurm-2038693.out
RNAseq/2023_AL_RNAseq/Script testing/slurm-2038694.out
RNAseq/2023_AL_RNAseq/Script testing/slurm-2038695.out
RNAseq/2023_AL_RNAseq/Script testing/slurm-2038705.out
RNAseq/2023_AL_RNAseq/Script testing/standaloneR.sh
RNAseq/2023_AL_RNAseq/Script testing/figures/
RNAseq/2023_AL_RNAseq/Script testing/figures/overexpressed_lowest_category.svg
RNAseq/2023_AL_RNAseq/Script testing/figures/pcaplot.svg
RNAseq/2023_AL_RNAseq/Script testing/figures/volcanoplot.svg
RNAseq/2023_MM_RNAseq/
RNAseq/2023_MM_RNAseq/bowtie_build.sh
RNAseq/2023_MM_RNAseq/condition1_scrismonoana_counts1.txt
RNAseq/2023_MM_RNAseq/condition1_scrismonoana_counts2.txt
RNAseq/2023_MM_RNAseq/condition2_cmatr_scris_ana_counts1.txt
RNAseq/2023_MM_RNAseq/condition2_cmatr_scris_ana_counts2.txt
RNAseq/2023_MM_RNAseq/deseq_tablesandkegg.R
RNAseq/2023_MM_RNAseq/may2020_kegg.csv
RNAseq/2023_MM_RNAseq/paired_end_duplicate_analysis.sh
RNAseq/2023_MM_RNAseq/scristatus.gff
RNAseq/2023_MM_RNAseq/scristatus_ko.txt
RNAseq/2023_MM_RNAseq/standaloneR.sh
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/cmatr.gff
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/cmatr_ko.txt
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/condition1_cmatrmonoana_counts1.txt
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/condition1_cmatrmonoana_counts2.txt
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/condition2_cmatr_scris_ana_counts1.txt
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/condition2_cmatr_scris_ana_counts2.txt
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/slurm-272398.out
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/figures/
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/figures/overexpressed_highest_category.svg
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/figures/overexpressed_lowest_category.svg
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/figures/pcaplot.svg
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/figures/repressed_highest_category.svg
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/figures/repressed_lowest_category.svg
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/figures/volcanoplot.svg
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/kegg_analysis/
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/kegg_analysis/allsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/kegg_analysis/downsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/kegg_analysis/overexpressed_kegg_summary_cathigh.csv
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/kegg_analysis/overexpressed_kegg_summary_catlow.csv
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/kegg_analysis/raw_kegg_table.csv
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/kegg_analysis/repressed_kegg_summary_cathigh.csv
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/kegg_analysis/repressed_kegg_summary_catlow.csv
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/kegg_analysis/upsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/rnaseq_analysis/
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/rnaseq_analysis/allsig_conditon2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/rnaseq_analysis/downsig_conditon2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/rnaseq_analysis/raw_condition2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/rnaseq_analysis/raw_deseqtable.csv
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/rnaseq_analysis/upsig_conditon2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/condition1_smitimonoaero_counts1.txt
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/condition1_smitimonoaero_counts2.txt
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/condition2_smitimonoana_counts1.txt
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/condition2_smitimonoana_counts2.txt
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/deseq_tablesandkegg.R
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/may2020_kegg.csv
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/slurm-272599.out
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/slurm-272600.out
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/smitis.gff
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/smitis_ko.txt
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/standaloneR.sh
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/figures/
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/figures/overexpressed_highest_category.svg
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/figures/overexpressed_lowest_category.svg
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/figures/pcaplot.svg
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/figures/repressed_highest_category.svg
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/figures/repressed_lowest_category.svg
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/figures/volcanoplot.svg
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/kegg_analysis/
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/kegg_analysis/allsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/kegg_analysis/downsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/kegg_analysis/overexpressed_kegg_summary_cathigh.csv
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/kegg_analysis/overexpressed_kegg_summary_catlow.csv
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/kegg_analysis/raw_kegg_table.csv
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/kegg_analysis/repressed_kegg_summary_cathigh.csv
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/kegg_analysis/repressed_kegg_summary_catlow.csv
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/kegg_analysis/upsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/rnaseq_analysis/
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/rnaseq_analysis/allsig_conditon2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/rnaseq_analysis/downsig_conditon2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/rnaseq_analysis/raw_condition2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/rnaseq_analysis/raw_deseqtable.csv
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/rnaseq_analysis/upsig_conditon2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/condition1_smitimonoaero_counts1.txt
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/condition1_smitimonoaero_counts2.txt
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/condition2_HP_smiti_aero_counts1.txt
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/condition2_HP_smiti_aero_counts2.txt
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/deseq_tablesandkegg.R
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/may2020_kegg.csv
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/paired_end_duplicate_analysis.sh
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/slurm-272603.out
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/smitis.gff
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/smitis_ko.txt
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/standaloneR.sh
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/figures/
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/figures/overexpressed_highest_category.svg
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/figures/overexpressed_lowest_category.svg
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/figures/pcaplot.svg
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/figures/repressed_highest_category.svg
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/figures/repressed_lowest_category.svg
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/figures/volcanoplot.svg
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/kegg_analysis/
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/kegg_analysis/allsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/kegg_analysis/downsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/kegg_analysis/overexpressed_kegg_summary_cathigh.csv
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/kegg_analysis/overexpressed_kegg_summary_catlow.csv
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/kegg_analysis/raw_kegg_table.csv
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/kegg_analysis/repressed_kegg_summary_cathigh.csv
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/kegg_analysis/repressed_kegg_summary_catlow.csv
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/kegg_analysis/upsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/rnaseq_analysis/
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/rnaseq_analysis/allsig_conditon2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/rnaseq_analysis/downsig_conditon2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/rnaseq_analysis/raw_condition2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/rnaseq_analysis/raw_deseqtable.csv
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/rnaseq_analysis/upsig_conditon2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/condition1_smitimonoana_counts1.txt
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/condition1_smitimonoana_counts2.txt
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/condition2_HP_smiti_anaero_counts1.txt
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/condition2_HP_smiti_anaero_counts2.txt
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/deseq_tablesandkegg.R
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/may2020_kegg.csv
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/paired_end_duplicate_analysis.sh
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/slurm-272606.out
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/smitis.gff
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/smitis_ko.txt
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/standaloneR.sh
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/figures/
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/figures/overexpressed_highest_category.svg
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/figures/overexpressed_lowest_category.svg
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/figures/pcaplot.svg
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/figures/repressed_highest_category.svg
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/figures/repressed_lowest_category.svg
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/figures/volcanoplot.svg
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/kegg_analysis/
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/kegg_analysis/allsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/kegg_analysis/downsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/kegg_analysis/overexpressed_kegg_summary_cathigh.csv
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/kegg_analysis/overexpressed_kegg_summary_catlow.csv
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/kegg_analysis/raw_kegg_table.csv
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/kegg_analysis/repressed_kegg_summary_cathigh.csv
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/kegg_analysis/repressed_kegg_summary_catlow.csv
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/kegg_analysis/upsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/rnaseq_analysis/
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/rnaseq_analysis/allsig_conditon2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/rnaseq_analysis/downsig_conditon2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/rnaseq_analysis/raw_condition2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/rnaseq_analysis/raw_deseqtable.csv
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/rnaseq_analysis/upsig_conditon2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/2023_kegg.csv
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/ATCC_ko.txt
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/README.md
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/condition1_HP_counts1.txt
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/condition1_HP_counts2.txt
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/condition2_HPSM_counts1.txt
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/condition2_HPSM_counts2.txt
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/deseq_tablesandkegg.R
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/id.txt
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/index.gff
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/paired_end_2_vs_3_reps.sh
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/paired_end_2_vs_4_reps.sh
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/paired_end_duplicate_analysis.sh
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/paired_end_triplicate.sh
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/slurm-258912.out
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/slurm-258913.out
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/slurm-258915.out
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/slurm-258934.out
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/slurm-258936.out
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/slurm-258944.out
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/slurm-258951.out
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/slurm-259020.out
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/slurm-259027.out
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/slurm-259028.out
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/slurm-259029.out
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/standaloneR.sh
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/HEAD
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/config
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/description
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/index
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/packed-refs
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/hooks/
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/hooks/applypatch-msg.sample
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/hooks/commit-msg.sample
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/hooks/fsmonitor-watchman.sample
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/hooks/post-update.sample
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/hooks/pre-applypatch.sample
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/hooks/pre-commit.sample
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/hooks/pre-merge-commit.sample
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/hooks/pre-push.sample
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/hooks/pre-rebase.sample
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/hooks/pre-receive.sample
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/hooks/prepare-commit-msg.sample
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/hooks/push-to-checkout.sample
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/hooks/update.sample
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/info/
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/info/exclude
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/logs/
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/logs/HEAD
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/logs/refs/
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/logs/refs/heads/
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/logs/refs/heads/master
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/logs/refs/remotes/
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/logs/refs/remotes/origin/
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/logs/refs/remotes/origin/HEAD
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/objects/
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/objects/pack/
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/objects/pack/pack-c6626ba4db1b228af23dc23ec7ee5d241a7a1388.idx
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/objects/pack/pack-c6626ba4db1b228af23dc23ec7ee5d241a7a1388.pack
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/refs/
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/refs/heads/
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/refs/heads/master
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/refs/remotes/
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/refs/remotes/origin/
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/refs/remotes/origin/HEAD
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/index/
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/index/.1.bt2
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/index/.2.bt2
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/index/.3.bt2
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/index/.4.bt2
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/index/.rev.1.bt2
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/index/.rev.2.bt2
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/index/atcc_hpara.fna
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/index/hp_index.1.bt2
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/index/hp_index.2.bt2
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/index/hp_index.3.bt2
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/index/hp_index.4.bt2
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/index/hp_index.rev.1.bt2
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/index/hp_index.rev.2.bt2
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/index/testbuild.1.bt2
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/index/testbuild.2.bt2
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/index/testbuild.3.bt2
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/index/testbuild.4.bt2
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/index/testbuild.rev.1.bt2
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/index/testbuild.rev.2.bt2
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/condition1_scrismonoaero_counts1.txt
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/condition1_scrismonoaero_counts2.txt
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/condition2_cmatr_scris_aero_counts1.txt
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/condition2_cmatr_scris_aero_counts2.txt
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/figures/
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/figures/overexpressed_highest_category.svg
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/figures/overexpressed_lowest_category.svg
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/figures/pcaplot.svg
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/figures/repressed_highest_category.svg
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/figures/repressed_lowest_category.svg
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/figures/volcanoplot.svg
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/kegg_analysis/
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/kegg_analysis/allsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/kegg_analysis/downsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/kegg_analysis/overexpressed_kegg_summary_cathigh.csv
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/kegg_analysis/overexpressed_kegg_summary_catlow.csv
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/kegg_analysis/raw_kegg_table.csv
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/kegg_analysis/repressed_kegg_summary_cathigh.csv
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/kegg_analysis/repressed_kegg_summary_catlow.csv
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/kegg_analysis/upsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/rnaseq_analysis/
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/rnaseq_analysis/allsig_conditon2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/rnaseq_analysis/downsig_conditon2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/rnaseq_analysis/raw_condition2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/rnaseq_analysis/raw_deseqtable.csv
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/rnaseq_analysis/upsig_conditon2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/condition1_scrismonoaero_counts1.txt
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/condition1_scrismonoaero_counts2.txt
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/condition2_scrismonoana_counts1.txt
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/condition2_scrismonoana_counts2.txt
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/deseq_tablesandkegg.R
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/may2020_kegg.csv
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/slurm-277182.out
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/slurm-277183.out
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/standaloneR.sh
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/figures/
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/figures/overexpressed_highest_category.svg
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/figures/overexpressed_lowest_category.svg
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/figures/pcaplot.svg
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/figures/repressed_highest_category.svg
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/figures/repressed_lowest_category.svg
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/figures/volcanoplot.svg
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/kegg_analysis/
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/kegg_analysis/allsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/kegg_analysis/downsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/kegg_analysis/overexpressed_kegg_summary_cathigh.csv
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/kegg_analysis/overexpressed_kegg_summary_catlow.csv
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/kegg_analysis/raw_kegg_table.csv
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/kegg_analysis/repressed_kegg_summary_cathigh.csv
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/kegg_analysis/repressed_kegg_summary_catlow.csv
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/kegg_analysis/upsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/rnaseq_analysis/
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/rnaseq_analysis/allsig_conditon2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/rnaseq_analysis/downsig_conditon2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/rnaseq_analysis/raw_condition2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/rnaseq_analysis/raw_deseqtable.csv
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/rnaseq_analysis/upsig_conditon2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/condition1_scrismonoana_counts1.txt
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/condition1_scrismonoana_counts2.txt
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/condition2_cmatr_scris_ana_counts1.txt
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/condition2_cmatr_scris_ana_counts2.txt
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/deseq_tablesandkegg.R
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/may2020_kegg.csv
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/scristatus.gff
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/scristatus_ko.txt
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/slurm-277258.out
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/slurm-277259.out
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/standaloneR.sh
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/figures/
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/figures/overexpressed_lowest_category.svg
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/figures/pcaplot.svg
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/figures/volcanoplot.svg
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/kegg_analysis/
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/kegg_analysis/allsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/kegg_analysis/downsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/kegg_analysis/raw_kegg_table.csv
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/kegg_analysis/upsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/rnaseq_analysis/
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/rnaseq_analysis/allsig_conditon2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/rnaseq_analysis/downsig_conditon2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/rnaseq_analysis/raw_condition2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/rnaseq_analysis/raw_deseqtable.csv
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/rnaseq_analysis/upsig_conditon2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/bowtie_build.sh
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/condition1_smitimonoaero_counts1.txt
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/condition1_smitimonoaero_counts2.txt
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/condition2_cmatr_smiti_aero_counts1.txt
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/condition2_cmatr_smiti_aero_counts2.txt
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/deseq_tablesandkegg.R
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/may2020_kegg.csv
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/paired_end_duplicate_analysis.sh
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/slurm-289250.out
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/slurm-289251.out
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/smitis.gff
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/smitis_ko.txt
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/standaloneR.sh
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/figures/
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/figures/overexpressed_highest_category.svg
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/figures/overexpressed_lowest_category.svg
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/figures/pcaplot.svg
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/figures/repressed_highest_category.svg
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/figures/repressed_lowest_category.svg
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/figures/volcanoplot.svg
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/kegg_analysis/
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/kegg_analysis/allsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/kegg_analysis/downsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/kegg_analysis/overexpressed_kegg_summary_cathigh.csv
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/kegg_analysis/overexpressed_kegg_summary_catlow.csv
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/kegg_analysis/raw_kegg_table.csv
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/kegg_analysis/repressed_kegg_summary_cathigh.csv
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/kegg_analysis/repressed_kegg_summary_catlow.csv
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/kegg_analysis/upsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/rnaseq_analysis/
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/rnaseq_analysis/allsig_conditon2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/rnaseq_analysis/downsig_conditon2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/rnaseq_analysis/raw_condition2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/rnaseq_analysis/raw_deseqtable.csv
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/rnaseq_analysis/upsig_conditon2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/Tools/
RNAseq/2023_MM_RNAseq/Tools/smitis.gff
RNAseq/2023_MM_RNAseq/Tools/smitis_ko.txt
RNAseq/2023_MM_RNAseq/figures/
RNAseq/2023_MM_RNAseq/figures/overexpressed_lowest_category.svg
RNAseq/2023_MM_RNAseq/figures/pcaplot.svg
RNAseq/2023_MM_RNAseq/figures/volcanoplot.svg
RNAseq/2023_MM_RNAseq/kegg_analysis/
RNAseq/2023_MM_RNAseq/kegg_analysis/allsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_MM_RNAseq/kegg_analysis/downsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_MM_RNAseq/kegg_analysis/raw_kegg_table.csv
RNAseq/2023_MM_RNAseq/kegg_analysis/upsig_condition2_vs_condition1_kegg.csv
RNAseq/2023_MM_RNAseq/rnaseq_analysis/
RNAseq/2023_MM_RNAseq/rnaseq_analysis/allsig_conditon2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/rnaseq_analysis/downsig_conditon2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/rnaseq_analysis/raw_condition2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/rnaseq_analysis/raw_deseqtable.csv
RNAseq/2023_MM_RNAseq/rnaseq_analysis/upsig_conditon2_vs_condition1.csv
RNAseq/2023_MM_RNAseq/slurms/
RNAseq/2023_MM_RNAseq/slurms/slurm-272572.out
RNAseq/2023_MM_RNAseq/slurms/slurm-272573.out
RNAseq/2023_MM_RNAseq/slurms/slurm-272579.out
RNAseq/2023_MM_RNAseq/slurms/slurm-272593.out
RNAseq/2023_MM_RNAseq/slurms/slurm-272594.out
RNAseq/2023_MM_RNAseq/slurms/slurm-272595.out
RNAseq/2023_MM_RNAseq/slurms/slurm-274393.out
RNAseq/2023_MM_RNAseq/slurms/slurm-274395.out
RNAseq/2023_MM_RNAseq/slurms/slurm-274866.out
RNAseq/2023_MM_RNAseq/slurms/slurm-274872.out
RNAseq/2023_MM_RNAseq/slurms/slurm-277185.out
RNAseq/2023_MM_RNAseq/slurms/slurm-277186.out
RNAseq/2023_MM_RNAseq/slurms/slurm-277187.out
RNAseq/2023_MM_RNAseq/slurms/slurm-277190.out
RNAseq/2023_MM_RNAseq/slurms/slurm-277262.out
RNAseq/2024_valm/
RNAseq/2024_valm/anaes_cmat/
RNAseq/2024_valm/anaes_cmat/MR_rnaseq_v3.sh
RNAseq/2024_valm/anaes_cmat/anaes.gff
RNAseq/2024_valm/anaes_cmat/anaes_ko.txt
RNAseq/2024_valm/anaes_cmat/condition1_an_monocult_counts1.txt
RNAseq/2024_valm/anaes_cmat/condition1_an_monocult_counts2.txt
RNAseq/2024_valm/anaes_cmat/condition1_an_monocult_counts3.txt
RNAseq/2024_valm/anaes_cmat/condition2_an_cocult_counts1.txt
RNAseq/2024_valm/anaes_cmat/condition2_an_cocult_counts2.txt
RNAseq/2024_valm/anaes_cmat/condition2_an_cocult_counts3.txt
RNAseq/2024_valm/anaes_cmat/deseq_tablesandkegg.R
RNAseq/2024_valm/anaes_cmat/may2020_kegg.csv
RNAseq/2024_valm/anaes_cmat/metadata.tsv
RNAseq/2024_valm/anaes_cmat/slurm-324068.out
RNAseq/2024_valm/anaes_cmat/alignment/
RNAseq/2024_valm/anaes_cmat/alignment/1BB_S175_.bam
RNAseq/2024_valm/anaes_cmat/alignment/1BB_S175_.sam
RNAseq/2024_valm/anaes_cmat/alignment/2BB_S176_.bam
RNAseq/2024_valm/anaes_cmat/alignment/2BB_S176_.sam
RNAseq/2024_valm/anaes_cmat/alignment/3BB_S177_.bam
RNAseq/2024_valm/anaes_cmat/alignment/3BB_S177_.sam
RNAseq/2024_valm/anaes_cmat/alignment/A1BB_S172_.bam
RNAseq/2024_valm/anaes_cmat/alignment/A1BB_S172_.sam
RNAseq/2024_valm/anaes_cmat/alignment/A2BB_S173_.bam
RNAseq/2024_valm/anaes_cmat/alignment/A2BB_S173_.sam
RNAseq/2024_valm/anaes_cmat/alignment/A3BB_S174_.bam
RNAseq/2024_valm/anaes_cmat/alignment/A3BB_S174_.sam
RNAseq/2024_valm/anaes_cmat/alignment/mdsum.txt
RNAseq/2024_valm/anaes_cmat/alignment/nohup.out
RNAseq/2024_valm/anaes_cmat/alignment/sam2bam.sh
RNAseq/2024_valm/anaes_cmat/figures/
RNAseq/2024_valm/anaes_cmat/figures/overexpressed_highest_category.svg
RNAseq/2024_valm/anaes_cmat/figures/overexpressed_lowest_category.svg
RNAseq/2024_valm/anaes_cmat/figures/pcaplot.svg
RNAseq/2024_valm/anaes_cmat/figures/repressed_highest_category.svg
RNAseq/2024_valm/anaes_cmat/figures/repressed_lowest_category.svg
RNAseq/2024_valm/anaes_cmat/figures/volcanoplot.svg
RNAseq/2024_valm/anaes_cmat/kegg_analysis/
RNAseq/2024_valm/anaes_cmat/kegg_analysis/allsig_condition2_vs_condition1_kegg.csv
RNAseq/2024_valm/anaes_cmat/kegg_analysis/downsig_condition2_vs_condition1_kegg.csv
RNAseq/2024_valm/anaes_cmat/kegg_analysis/overexpressed_kegg_summary_cathigh.csv
RNAseq/2024_valm/anaes_cmat/kegg_analysis/overexpressed_kegg_summary_catlow.csv
RNAseq/2024_valm/anaes_cmat/kegg_analysis/raw_kegg_table.csv
RNAseq/2024_valm/anaes_cmat/kegg_analysis/repressed_kegg_summary_cathigh.csv
RNAseq/2024_valm/anaes_cmat/kegg_analysis/repressed_kegg_summary_catlow.csv
RNAseq/2024_valm/anaes_cmat/kegg_analysis/upsig_condition2_vs_condition1_kegg.csv
RNAseq/2024_valm/anaes_cmat/rnaseq_analysis/
RNAseq/2024_valm/anaes_cmat/rnaseq_analysis/allsig_conditon2_vs_condition1.csv
RNAseq/2024_valm/anaes_cmat/rnaseq_analysis/downsig_conditon2_vs_condition1.csv
RNAseq/2024_valm/anaes_cmat/rnaseq_analysis/raw_condition2_vs_condition1.csv
RNAseq/2024_valm/anaes_cmat/rnaseq_analysis/raw_deseqtable.csv
RNAseq/2024_valm/anaes_cmat/rnaseq_analysis/upsig_conditon2_vs_condition1.csv
RNAseq/2024_valm/cmat_anaes/
RNAseq/2024_valm/cmat_anaes/MR_rnaseq_v2.sh
RNAseq/2024_valm/cmat_anaes/cmatr.gff
RNAseq/2024_valm/cmat_anaes/cmatr_ko.txt
RNAseq/2024_valm/cmat_anaes/condition1_cm_monocult_counts1.txt
RNAseq/2024_valm/cmat_anaes/condition1_cm_monocult_counts2.txt
RNAseq/2024_valm/cmat_anaes/condition2_cm_anaes_cocult_counts1.txt
RNAseq/2024_valm/cmat_anaes/condition2_cm_anaes_cocult_counts2.txt
RNAseq/2024_valm/cmat_anaes/condition2_cm_anaes_cocult_counts3.txt
RNAseq/2024_valm/cmat_anaes/deseq_tablesandkegg.R
RNAseq/2024_valm/cmat_anaes/may2020_kegg.csv
RNAseq/2024_valm/cmat_anaes/metadata.tsv
RNAseq/2024_valm/cmat_anaes/null.txt
RNAseq/2024_valm/cmat_anaes/slurm-318277.out
RNAseq/2024_valm/cmat_anaes/alignment/
RNAseq/2024_valm/cmat_anaes/alignment/1BB_S175_.bam
RNAseq/2024_valm/cmat_anaes/alignment/1BB_S175_.sam
RNAseq/2024_valm/cmat_anaes/alignment/2BB_S176_.bam
RNAseq/2024_valm/cmat_anaes/alignment/2BB_S176_.sam
rsync error: received SIGUSR1 (code 19) at main.c(1600) [generator=3.4.1]
rsync error: received SIGINT, SIGTERM, or SIGHUP (code 20) at rsync.c(716) [sender=3.4.1]
rsync: [receiver] write error: Broken pipe (32)