sending incremental file list
16S/
16S/Rexport/
16S/Rexport/AF-hum-table.biom/
16S/Rexport/NP-hum-table.biom/
16S/Rexport/SF-hum-table.biom/
16S/Rexport/minF-hum-table.biom/
16S/SF-hum/
16S/SF-hum/core-metrics-results-latest/
16S/SF-hum/core-metrics-results/
16S/Test runs 16s AL/
16S/Test runs 16s AL/Master-Filtered/
16S/Test runs 16s AL/Master-Filtered/master-core-metrics-results-HAvPS/
16S/Test runs 16s AL/MinFil_AL/
16S/Test runs 16s AL/al_2021_2/
16S/Test runs 16s AL/al_2022_1/
16S/Test runs 16s AL/al_2022_1_CMR/
16S/Test runs 16s AL/al_2022_1_CMR/core-metrics-results/
16S/Test runs 16s AL/al_2022_2_CMR/
16S/Test runs 16s AL/al_2022_2_CMR/core-metrics-results-2/
16S/Test runs 16s AL/al_2022_2_CMR/core-metrics-results-3/
16S/Test runs 16s AL/al_2022_2_CMR/core-metrics-results-4/
16S/Test runs 16s AL/al_2022_2_CMR/core-metrics-results-5/
16S/Test runs 16s AL/al_2022_2_CMR/core-metrics-results/
16S/Test runs 16s AL/ctrl-filter-AL/
16S/Test runs 16s AL/fil-media-2/
16S/Test runs 16s AL/fil-media-3/
16S/Test runs 16s AL/fil-media/
16S/Test runs 16s AL/fil-nocontrol/
16S/Test runs 16s AL/filtered-hydroxyapatite/
16S/Test runs 16s AL/filtered-polystyrene/
16S/Test runs 16s AL/metadata-filter-AL/
16S/Test runs 16s AL/taxon-filtered/
16S/classifiers/
16S/classifiers/Older_serum/
16S/classifiers/SILVA_132_QIIME_release/
16S/classifiers/SILVA_132_QIIME_release/core_alignment/
16S/classifiers/SILVA_132_QIIME_release/raw_data/
16S/classifiers/SILVA_132_QIIME_release/rep_set/
16S/classifiers/SILVA_132_QIIME_release/rep_set/rep_set_16S_only/
16S/classifiers/SILVA_132_QIIME_release/rep_set/rep_set_16S_only/90/
16S/classifiers/SILVA_132_QIIME_release/rep_set/rep_set_16S_only/94/
16S/classifiers/SILVA_132_QIIME_release/rep_set/rep_set_16S_only/97/
16S/classifiers/SILVA_132_QIIME_release/rep_set/rep_set_16S_only/99/
16S/classifiers/SILVA_132_QIIME_release/rep_set/rep_set_18S_only/
16S/classifiers/SILVA_132_QIIME_release/rep_set/rep_set_18S_only/90/
16S/classifiers/SILVA_132_QIIME_release/rep_set/rep_set_18S_only/94/
16S/classifiers/SILVA_132_QIIME_release/rep_set/rep_set_18S_only/97/
16S/classifiers/SILVA_132_QIIME_release/rep_set/rep_set_18S_only/99/
16S/classifiers/SILVA_132_QIIME_release/rep_set/rep_set_all/
16S/classifiers/SILVA_132_QIIME_release/rep_set/rep_set_all/90/
16S/classifiers/SILVA_132_QIIME_release/rep_set/rep_set_all/94/
16S/classifiers/SILVA_132_QIIME_release/rep_set/rep_set_all/97/
16S/classifiers/SILVA_132_QIIME_release/rep_set/rep_set_all/99/
16S/classifiers/SILVA_132_QIIME_release/rep_set_aligned/
16S/classifiers/SILVA_132_QIIME_release/rep_set_aligned/90/
16S/classifiers/SILVA_132_QIIME_release/rep_set_aligned/94/
16S/classifiers/SILVA_132_QIIME_release/rep_set_aligned/97/
16S/classifiers/SILVA_132_QIIME_release/rep_set_aligned/99/
16S/classifiers/SILVA_132_QIIME_release/taxonomy/
16S/classifiers/SILVA_132_QIIME_release/taxonomy/16S_only/
16S/classifiers/SILVA_132_QIIME_release/taxonomy/16S_only/90/
16S/classifiers/SILVA_132_QIIME_release/taxonomy/16S_only/94/
16S/classifiers/SILVA_132_QIIME_release/taxonomy/16S_only/97/
16S/classifiers/SILVA_132_QIIME_release/taxonomy/16S_only/99/
16S/classifiers/SILVA_132_QIIME_release/taxonomy/18S_only/
16S/classifiers/SILVA_132_QIIME_release/taxonomy/18S_only/90/
16S/classifiers/SILVA_132_QIIME_release/taxonomy/18S_only/94/
16S/classifiers/SILVA_132_QIIME_release/taxonomy/18S_only/97/
16S/classifiers/SILVA_132_QIIME_release/taxonomy/18S_only/99/
16S/classifiers/SILVA_132_QIIME_release/taxonomy/taxonomy_all/
16S/classifiers/SILVA_132_QIIME_release/taxonomy/taxonomy_all/90/
16S/classifiers/SILVA_132_QIIME_release/taxonomy/taxonomy_all/94/
16S/classifiers/SILVA_132_QIIME_release/taxonomy/taxonomy_all/97/
16S/classifiers/SILVA_132_QIIME_release/taxonomy/taxonomy_all/99/
16S/classifiers/SILVA_132_QIIME_release/trees/
16S/classifiers/SILVA_132_QIIME_release/trees/90/
16S/classifiers/SILVA_132_QIIME_release/trees/94/
16S/classifiers/SILVA_132_QIIME_release/trees/97/
16S/classifiers/SILVA_132_QIIME_release/trees/99/
16S/classifiers/custom_classifer/
16S/classifiers/homd-classifier/
16S/classifiers/homd-classifier/HOMD-classifier.tsv/
16S/classifiers/homd-classifier/HOMD-classifier/
16S/classifiers/homd-classifier/exported-taxa/
16S/classifiers/silva-taxonomy-AL/
16S/classifiers/silva-taxonomy-AL/silva-taxonomy-AL/
16S/classifiers/silva-taxonomy-AL2023/
16S/classifiers/silva-taxonomy/
16S/classifiers/silva-taxonomy_AL_2024/
16S/metadata/
16S/proc_reads/
16S/proc_reads/2022_AL_SUPP/
16S/proc_reads/2022_AL_SUPP/2022/
16S/proc_reads/2022_AL_SUPP/2022PLEASEFORETHELOVEOFHGOD/
16S/proc_reads/2022_AL_SUPP/2022sample-name/
16S/proc_reads/2022_AL_SUPP/2022timepoints3/
16S/proc_reads/2022_AL_SUPP/Master-Filtered/
16S/proc_reads/2022_AL_SUPP/Master-Filtered/master-core-metrics-results-HA_media/
16S/proc_reads/2022_AL_SUPP/Master-Filtered/master-core-metrics-results-HAvPS/
16S/proc_reads/2022_AL_SUPP/fil-nocontrol/
16S/proc_reads/2022_AL_SUPP/fil-nocontrolv1v2/
16S/proc_reads/2022_AL_SUPP/filteredsamples_2022/
16S/proc_reads/2022_AL_SUPP/filteredsamples_2022/core-metrics-results-1000/
16S/proc_reads/2022_AL_SUPP/filteredsamples_2022/core-metrics-results-2022/
16S/proc_reads/2022_AL_SUPP/filteredsamples_2022/core-metrics-results-2022222222222222222222222222/
16S/proc_reads/2022_AL_SUPP/filteredsamples_2022/core-metrics-results/
16S/proc_reads/2022_AL_SUPP/filteredsamples_2022_salivacore-metrics-results-A-Saliva/
16S/proc_reads/2022_AL_SUPP/filteredsamples_2022core-metrics-results-1000/
16S/proc_reads/2022_AL_SUPP/master-core-metrics-results-paired/
16S/proc_reads/2022_AL_SUPP/master-core-metrics-results-v1v2/
16S/proc_reads/2023_AL_Master/
16S/proc_reads/2023_AL_Master/2023_MasterFilteredSamples/
16S/proc_reads/2023_AL_Master/FilteredSamples/
16S/proc_reads/2023_AL_Master/core-metric-results-8000/
16S/proc_reads/2023_AL_Master/core-metric-results-subjectA/
16S/proc_reads/2023_AL_Master/core-metric-results-subjectAn/
16S/proc_reads/2023_AL_Master/core-metric-results-subjectJ/
16S/proc_reads/2023_AL_Master/core-metric-results-subjectS/
16S/proc_reads/2023_AL_Master/core-metric-results/
16S/proc_reads/2023_AL_Master/pseudo-trip-data/
16S/proc_reads/2023_AL_Master/pseudo-trip-data/core-metric-results-A/
16S/proc_reads/2023_AL_Master/pseudo-trip-data/core-metric-results-An/
16S/proc_reads/2023_AL_Master/pseudo-trip-data/core-metric-results-J/
16S/proc_reads/2023_AL_Master/pseudo-trip-data/core-metric-results-S/
16S/proc_reads/2024_AL_SUPP_13610/
16S/proc_reads/2024_AL_SUPP_13610/medias/
16S/proc_reads/2024_AL_SUPP_6000/
16S/proc_reads/2024_AL_SUPP_6000/BS5T0/
16S/proc_reads/2024_AL_SUPP_6000/BSFS/
16S/proc_reads/2024_AL_SUPP_6000/BST0/
16S/proc_reads/2024_AL_SUPP_6000/FS5BS5/
16S/proc_reads/2024_AL_SUPP_6000/FS5T0/
16S/proc_reads/2024_AL_SUPP_6000/FSBS/
16S/proc_reads/2024_AL_SUPP_6000/FST0/
16S/proc_reads/2024_AL_SUPP_6000/filtered-only/
16S/proc_reads/2024_AL_SUPP_6000/filteredsamples_2024-2/
16S/proc_reads/2024_AL_SUPP_6000/filteredsamples_2024/
16S/proc_reads/2024_AL_SUPP_6000/filteredsamples_2024_3/
16S/proc_reads/2024_AL_SUPP_6000/medias/
16S/proc_reads/2024_AL_SUPP_9640/
16S/proc_reads/2024_AL_SUPP_9640/media/
16S/proc_reads/AF-hum/
16S/proc_reads/AF-hum/core-metrics-results-latest/
16S/proc_reads/AF-hum/core-metrics-results/
16S/proc_reads/MinFilPlaque/
16S/proc_reads/MockQC/
16S/proc_reads/NP-hum/
16S/proc_reads/NP-hum/core-metrics-results-latest/
16S/proc_reads/NP-hum/core-metrics-results/
16S/proc_reads/Older_serum/
16S/proc_reads/Older_serum/QC_Zymo/
16S/proc_reads/Older_serum/core-metrics-Filtered-Human/
16S/proc_reads/Older_serum/core-metrics-results-Run1/
16S/proc_reads/Older_serum/core-metrics-results-Run12/
16S/proc_reads/Older_serum/core-metrics-results-Run2/
16S/proc_reads/Older_serum/core-metrics-results-Run3/
16S/proc_reads/Older_serum/core-metrics-results-RunM-Human/
16S/proc_reads/Older_serum/core-metrics-results-RunM/
16S/proc_reads/Older_serum/filtered/
16S/proc_reads/Older_serum/filtered/control.collapse.frequency/
16S/proc_reads/Older_serum/filtered/core-metrics-results-Run3-HUMN/
16S/proc_reads/Older_serum/filtered/core-metrics-results-Run3-Mock/
16S/proc_reads/SF-hum/
16S/proc_reads/SF-hum/core-metrics-results-latest/
16S/proc_reads/SF-hum/core-metrics-results/
16S/proc_reads/core-metrics-results-initial/
16S/proc_reads/ctrl-filter/
16S/proc_reads/ctrl-filter/initial-human/
16S/proc_reads/minF-hum/
16S/proc_reads/minF-hum/core-metrics-results-latest/
16S/proc_reads/minF-hum/core-metrics-results/
16S/proc_reads/minF-hum/genomes/
16S/proc_reads/minF-hum/genomes/cmatr/
16S/proc_reads/minF-hum/genomes/hpara/
16S/proc_reads/minF-hum/genomes/hpara/Hpara_ATCC33392/
16S/proc_reads/minF-hum/genomes/hpara/Hpara_ATCC33392/DasithPerera210402/
16S/proc_reads/minF-hum/genomes/hpara/Hpara_ATCC33392/DasithPerera210402/Assembly/
16S/proc_reads/minF-hum/genomes/hpara/Hpara_ATCC33392/DasithPerera210402/Assembly/DP1/
16S/proc_reads/minF-hum/genomes/hpara/Hpara_ATCC33392/DasithPerera210402/Nanopore Reads/
16S/proc_reads/minF-hum/genomes/scris/
16S/proc_reads/minF-hum/genomes/scris/alignment/
16S/proc_reads/minF-hum/genomes/scris/old files/
16S/proc_reads/minF-hum/genomes/smiti/
16S/proc_reads/minF-hum/genomes/ssang/
16S/proc_reads/taxon-filtered/
16S/visualizations/
16S/visualizations/AL_2022/
16S/visualizations/AL_2023/
16S/visualizations/AL_2023/master-core-metrics-results-SubjectA-Saliva-only-200/
16S/visualizations/AL_2023/master-core-metrics-results-SubjectS-Saliva-only-6000/
16S/visualizations/AL_2024/
16S/visualizations/AL_2024/BS5T0-filtered/
16S/visualizations/AL_2024/BSFS-filtered/
16S/visualizations/AL_2024/BST0-filtered/
16S/visualizations/AL_2024/FS5BS5-filtered/
16S/visualizations/AL_2024/FS5T0-filtered/
16S/visualizations/AL_2024/FSBS-filtered/
16S/visualizations/AL_2024/FST0-filtered/
16S/visualizations/Older_serum/
RNAseq/
RNAseq/2018_EA_subging_gingivitis/
RNAseq/2018_EA_subging_gingivitis/figures/
RNAseq/2018_EA_subging_gingivitis/kegg_analysis/
RNAseq/2018_EA_subging_gingivitis/rnaseq_analysis/
RNAseq/2020_transcriptome_analyses_AL/
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/figures/
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/kegg_analysis/
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_aero/rnaseq_analysis/
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/figures/
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/kegg_analysis/
RNAseq/2020_transcriptome_analyses_AL/Data/sm_cm_coculture_alignment_ana/rnaseq_analysis/
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/figures/
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/kegg_analysis/
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_aero_vs_espinoza/rnaseq_analysis/
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/figures/
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/kegg_analysis/
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_alignment/rnaseq_analysis/
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/figures/
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/kegg_analysis/
RNAseq/2020_transcriptome_analyses_AL/Data/smhp_ana_vs_whiteley/rnaseq_analysis/
RNAseq/2020_transcriptome_analyses_AL/FastQ/
RNAseq/2020_transcriptome_analyses_AL/Sm_mono_aero_vs_ana/
RNAseq/2020_transcriptome_analyses_AL/Sm_mono_aero_vs_ana/figures/
RNAseq/2020_transcriptome_analyses_AL/Sm_mono_aero_vs_ana/kegg_analysis/
RNAseq/2020_transcriptome_analyses_AL/Sm_mono_aero_vs_ana/rnaseq_analysis/
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/figures/
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/kegg_analysis/
RNAseq/2020_transcriptome_analyses_AL/smhp_ana_vs_espinoza/rnaseq_analysis/
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/figures/
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/kegg_analysis/
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSCaero/rnaseq_analysis/
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/figures/
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/kegg_analysis/
RNAseq/2023_AL_RNAseq/2023_CM_AL/CMvsCMSMaero/rnaseq_analysis/
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/figures/
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/kegg_analysis/
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPaero_vs_HPana/rnaseq_analysis/
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/figures/
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/kegg_analysis/
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMaero/rnaseq_analysis/
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/figures/
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/kegg_analysis/
RNAseq/2023_AL_RNAseq/2023_HP_AL/HPvsHPSMana/rnaseq_analysis/
RNAseq/2023_AL_RNAseq/2023_HP_AL/hpara/
RNAseq/2023_AL_RNAseq/2023_SM_AL/
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMaero/
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMaero/figures/
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMaero/kegg_analysis/
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMaero/rnaseq_analysis/
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/figures/
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/kegg_analysis/
RNAseq/2023_AL_RNAseq/2023_SM_AL/SMvsHPSMana/rnaseq_analysis/
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis/
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/
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/kegg_analysis/
RNAseq/2023_AL_RNAseq/2023_SM_AL/smitis_mono_vs_cocult_aero/rnaseq_analysis/
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/figures/
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/newindex/
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Benitez_Meta/sm_BP2014/rnaseq_analysis/
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/figures/
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/kegg_analysis/
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/newindex/
RNAseq/2023_AL_RNAseq/2023_SM_aero_vs_Jorth_Meta_2014/rnaseq_analysis/
RNAseq/2023_AL_RNAseq/Script testing/
RNAseq/2023_AL_RNAseq/Script testing/figures/
RNAseq/2023_MM_RNAseq/
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/figures/
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/kegg_analysis/
RNAseq/2023_MM_RNAseq/CMvsCMSCanaero/rnaseq_analysis/
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/figures/
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/kegg_analysis/
RNAseq/2023_MM_RNAseq/NEW_SMaerovsSManaero/rnaseq_analysis/
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/figures/
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/kegg_analysis/
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSMaero/rnaseq_analysis/
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/figures/
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/kegg_analysis/
RNAseq/2023_MM_RNAseq/NEW_SMvsHPSManaero/rnaseq_analysis/
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/hooks/
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/info/
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/logs/
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/remotes/
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/logs/refs/remotes/origin/
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/refs/
RNAseq/2023_MM_RNAseq/RNASeq-analysis-toolkit/.git/refs/heads/
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/index/
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/figures/
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/kegg_analysis/
RNAseq/2023_MM_RNAseq/SCaerovsCMSCaero/rnaseq_analysis/
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/figures/
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/kegg_analysis/
RNAseq/2023_MM_RNAseq/SCaerovsScanaero/rnaseq_analysis/
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/figures/
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/kegg_analysis/
RNAseq/2023_MM_RNAseq/SCanaerovsCMSCanaero/rnaseq_analysis/
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/figures/
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/kegg_analysis/
RNAseq/2023_MM_RNAseq/SMaerovsCMSMaero/rnaseq_analysis/
RNAseq/2023_MM_RNAseq/Tools/
RNAseq/2023_MM_RNAseq/figures/
RNAseq/2023_MM_RNAseq/kegg_analysis/
RNAseq/2023_MM_RNAseq/rnaseq_analysis/
RNAseq/2023_MM_RNAseq/slurms/
RNAseq/2024_valm/
RNAseq/2024_valm/anaes_cmat/
RNAseq/2024_valm/anaes_cmat/alignment/
RNAseq/2024_valm/anaes_cmat/figures/
RNAseq/2024_valm/anaes_cmat/kegg_analysis/
RNAseq/2024_valm/anaes_cmat/rnaseq_analysis/
RNAseq/2024_valm/cmat_anaes/
RNAseq/2024_valm/cmat_anaes/alignment/
RNAseq/2024_valm/cmat_anaes/figures/
RNAseq/2024_valm/cmat_anaes/kegg_analysis/
RNAseq/2024_valm/cmat_anaes/rnaseq_analysis/
RNAseq/2024_valm/hk_cmat/
RNAseq/2024_valm/hk_cmat/alignment/
RNAseq/2024_valm/hk_cmat/figures/
RNAseq/2024_valm/hk_cmat/kegg_analysis/
RNAseq/2024_valm/hk_cmat/rnaseq_analysis/
RNAseq/EA21_alignment/
RNAseq/EA21_alignment/cmatDMmono_whiteleymeta/
RNAseq/EA21_alignment/cmatDMmono_whiteleymeta/figures/
RNAseq/EA21_alignment/cmatDMmono_whiteleymeta/kegg_analysis/
RNAseq/EA21_alignment/cmatDMmono_whiteleymeta/rnaseq_analysis/
RNAseq/EA21_alignment/cmatmono_sal/
RNAseq/EA21_alignment/cmatmono_sal/analysis/
RNAseq/EA21_alignment/cmatmono_sal/analysis/figures/
RNAseq/EA21_alignment/cmatmono_sal/analysis/kegg_analysis/
RNAseq/EA21_alignment/cmatmono_sal/analysis/richmono_cmsal/
RNAseq/EA21_alignment/cmatmono_sal/analysis/richmono_cmsal/figures/
RNAseq/EA21_alignment/cmatmono_sal/analysis/richmono_cmsal/kegg_analysis/
RNAseq/EA21_alignment/cmatmono_sal/analysis/richmono_cmsal/rnaseq_analysis/
RNAseq/EA21_alignment/cmatmono_sal/analysis/rnaseq_analysis/
RNAseq/EA21_alignment/cmatmono_sal/cmatsal_2014whiteleymeta/
RNAseq/EA21_alignment/cmatmono_sal/cmatsal_2014whiteleymeta/analysis/
RNAseq/EA21_alignment/cmatmono_sal/cmatsal_2014whiteleymeta/analysis/figures/
RNAseq/EA21_alignment/cmatmono_sal/cmatsal_2014whiteleymeta/analysis/kegg_analysis/
RNAseq/EA21_alignment/cmatmono_sal/cmatsal_2014whiteleymeta/analysis/rnaseq_analysis/
RNAseq/transcriptome_analyses/
RNAseq/transcriptome_analyses/2014whiteley_vs_hp/
RNAseq/transcriptome_analyses/2014whiteley_vs_hp/aerobic_vs_meta/
RNAseq/transcriptome_analyses/2014whiteley_vs_hp/aerobic_vs_meta/disease/
RNAseq/transcriptome_analyses/2014whiteley_vs_hp/aerobic_vs_meta/disease/figures/
RNAseq/transcriptome_analyses/2014whiteley_vs_hp/aerobic_vs_meta/disease/kegg_analysis/
RNAseq/transcriptome_analyses/2014whiteley_vs_hp/aerobic_vs_meta/disease/rnaseq_analysis/
RNAseq/transcriptome_analyses/2014whiteley_vs_hp/aerobic_vs_meta/figures/
RNAseq/transcriptome_analyses/2014whiteley_vs_hp/aerobic_vs_meta/kegg_analysis/
RNAseq/transcriptome_analyses/2014whiteley_vs_hp/aerobic_vs_meta/rnaseq_analysis/
RNAseq/transcriptome_analyses/2014whiteley_vs_hp/anaerobic_vs_meta/
RNAseq/transcriptome_analyses/2014whiteley_vs_hp/anaerobic_vs_meta/disease/
RNAseq/transcriptome_analyses/2014whiteley_vs_hp/anaerobic_vs_meta/disease/figures/
RNAseq/transcriptome_analyses/2014whiteley_vs_hp/anaerobic_vs_meta/disease/kegg_analysis/
RNAseq/transcriptome_analyses/2014whiteley_vs_hp/anaerobic_vs_meta/disease/rnaseq_analysis/
RNAseq/transcriptome_analyses/2014whiteley_vs_hp/anaerobic_vs_meta/figures/
RNAseq/transcriptome_analyses/2014whiteley_vs_hp/anaerobic_vs_meta/kegg_analysis/
RNAseq/transcriptome_analyses/2014whiteley_vs_hp/anaerobic_vs_meta/rnaseq_analysis/
RNAseq/transcriptome_analyses/aerobic_w_peroxide/
RNAseq/transcriptome_analyses/aerobic_w_peroxide/figures/
RNAseq/transcriptome_analyses/aerobic_w_peroxide/rnaseq_analysis/
RNAseq/transcriptome_analyses/completesequence/
RNAseq/transcriptome_analyses/completesequence/prokka_gff/
RNAseq/transcriptome_analyses/completesequence/prokka_gff/hp_anaero_vs_aero/
RNAseq/transcriptome_analyses/completesequence/prokka_gff/hp_sm_aerobic/
RNAseq/transcriptome_analyses/completesequence/rast_gff/
RNAseq/transcriptome_analyses/hp_anaero_vs_aero/
RNAseq/transcriptome_analyses/hp_anaero_vs_aero/figures/
RNAseq/transcriptome_analyses/hp_anaero_vs_aero/kegg_analysis/
RNAseq/transcriptome_analyses/hp_anaero_vs_aero/rnaseq_analysis/
RNAseq/transcriptome_analyses/hp_sm_aerobic/
RNAseq/transcriptome_analyses/hp_sm_aerobic/figures/
RNAseq/transcriptome_analyses/hp_sm_aerobic/kegg_analysis/
RNAseq/transcriptome_analyses/hp_sm_aerobic/rnaseq_analysis/
RNAseq/transcriptome_analyses/hpara_sm_anaerobic/
RNAseq/transcriptome_analyses/hpara_sm_anaerobic/figures/
RNAseq/transcriptome_analyses/hpara_sm_anaerobic/kegg_analysis/
RNAseq/transcriptome_analyses/hpara_sm_anaerobic/rnaseq_analysis/
RNAseq/transcriptome_analyses/oxyr/
RNAseq/transcriptome_analyses/oxyr/figures/
RNAseq/transcriptome_analyses/oxyr/kegg_analysis/
RNAseq/transcriptome_analyses/oxyr/rnaseq_analysis/
TnSeq_THP/
TnSeq_THP/MiSeq/
TnSeq_THP/MiSeq/MiSeq_TP1_TP20_TP50/
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TnSeq_THP/MiSeq/MiSeq_TP1_TP20_TP50/TP50/
TnSeq_THP/MiSeq/MiSeq_TP1_TP20_TP50/hpara/
TnSeq_THP/MiSeq/coculture_MiSeq/
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TnSeq_THP/MiSeq/coculture_MiSeq/TP10/
TnSeq_THP/MiSeq/coculture_MiSeq/TP11/
TnSeq_THP/MiSeq/coculture_MiSeq/TP12/
TnSeq_THP/MiSeq/coculture_MiSeq/TP13/
TnSeq_THP/MiSeq/coculture_MiSeq/TP14/
TnSeq_THP/MiSeq/coculture_MiSeq/TP15/
TnSeq_THP/MiSeq/coculture_MiSeq/TP2/
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TnSeq_THP/MiSeq/coculture_MiSeq/TP7/
TnSeq_THP/MiSeq/coculture_MiSeq/TP8/
TnSeq_THP/MiSeq/coculture_MiSeq/TP9/
TnSeq_THP/MiSeq/coculture_MiSeq/hpara/
TnSeq_THP/RNAseq/
TnSeq_THP/RNAseq/Aero_raw/
TnSeq_THP/RNAseq/Anaero_raw/
TnSeq_THP/RNAseq/MR_grant/
TnSeq_THP/RNAseq/MR_grant/alignment/
TnSeq_THP/RNAseq/MR_grant/hpara/
TnSeq_THP/RNAseq/MR_grant/hpmono_vs_cocult/
TnSeq_THP/RNAseq/MR_grant/hpmono_vs_cocult/figures/
TnSeq_THP/RNAseq/MR_grant/hpmono_vs_cocult/kegg_analysis/
TnSeq_THP/RNAseq/MR_grant/hpmono_vs_cocult/rnaseq_analysis/
TnSeq_THP/RNAseq/aero_vs_anaero/
TnSeq_THP/RNAseq/aero_vs_anaero/figures/
TnSeq_THP/RNAseq/aero_vs_anaero/kegg_analysis/
TnSeq_THP/RNAseq/aero_vs_anaero/rnaseq_analysis/
TnSeq_THP/RNAseq/aerobic_vs_meta_1/
TnSeq_THP/RNAseq/aerobic_vs_meta_1/disease/
TnSeq_THP/RNAseq/aerobic_vs_meta_1/figures/
TnSeq_THP/RNAseq/aerobic_vs_meta_1/kegg_analysis/
TnSeq_THP/RNAseq/aerobic_vs_meta_1/rnaseq_analysis/
TnSeq_THP/RNAseq/aerobic_vs_meta_2/
TnSeq_THP/RNAseq/aerobic_vs_meta_2/figures/
TnSeq_THP/RNAseq/aerobic_vs_meta_2/kegg_analysis/
TnSeq_THP/RNAseq/aerobic_vs_meta_2/rnaseq_analysis/
TnSeq_THP/RNAseq/ana_vs_meta_1/
TnSeq_THP/RNAseq/ana_vs_meta_1/figures/
TnSeq_THP/RNAseq/ana_vs_meta_1/kegg_analysis/
TnSeq_THP/RNAseq/ana_vs_meta_1/rnaseq_analysis/
TnSeq_THP/RNAseq/ana_vs_meta_2/
TnSeq_THP/RNAseq/ana_vs_meta_2/figures/
TnSeq_THP/RNAseq/ana_vs_meta_2/kegg_analysis/
TnSeq_THP/RNAseq/ana_vs_meta_2/rnaseq_analysis/
TnSeq_THP/RNAseq/figures/
TnSeq_THP/RNAseq/hp_raw_data/
TnSeq_THP/RNAseq/hpara/
TnSeq_THP/RNAseq/meta_2_counts/
TnSeq_THP/RNAseq/rnaseq_analysis/
TnSeq_THP/RNAseq/test/
TnSeq_THP/RNAseq/test2/
TnSeq_THP/RNAseq/test2/figures/
TnSeq_THP/RNAseq/test2/kegg_analysis/
TnSeq_THP/RNAseq/test2/rnaseq_analysis/
TnSeq_THP/RNAseq/test3/
TnSeq_THP/RNAseq/test3/figures/
TnSeq_THP/RNAseq/test3/kegg_analysis/
TnSeq_THP/RNAseq/test3/rnaseq_analysis/
TnSeq_THP/hp_atcc/
TnSeq_THP/hp_atcc/Absolute_essential/
TnSeq_THP/hp_atcc/Absolute_essential/Analyses/
TnSeq_THP/hp_atcc/Absolute_essential/Analyses/Hp_without_plasmid/
TnSeq_THP/hp_atcc/Absolute_essential/Analyses/Output_TA/
TnSeq_THP/hp_atcc/Absolute_essential/Analyses/Output_TAAT/
TnSeq_THP/hp_atcc/Absolute_essential/Analyses/Tp1_trimmed/
TnSeq_THP/hp_atcc/Absolute_essential/Analyses/Tp2_trimmed/
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TnSeq_THP/hp_atcc/After_quality_control/
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TnSeq_THP/hp_atcc/After_quality_control/data/Tp12_S12_R1_001_fastqc/
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TnSeq_THP/hp_atcc/atcc_absolute_essential/whole_genome/output/absolute/
TnSeq_THP/hp_oral_isolate/
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TnSeq_THP/hp_oral_isolate/Data/analyses/
TnSeq_THP/hp_oral_isolate/Data/analyses/Hp305/
TnSeq_THP/hp_oral_isolate/Data/analyses/Output/
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TnSeq_THP/serum_survival/Data/analyses_old/active_oi/TP9_S9_R1_001_trimmed/
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TnSeq_THP/snakemake/
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sent 406,966 bytes  received 5,400 bytes  35,857.91 bytes/sec
total size is 2,618,878,540,870  speedup is 6,350,859.53