#!/bin/bash
#SBATCH -t 12:00:00
#SBATCH --nodes=2 --ntasks-per-node=2
#SBATCH --export=NONE
#SBATCH --mem=96G
#SBATCH --mail-user=alex_labossiere@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL

module load R-bundle-Bioconductor/3.10-foss-2019b
module load Bowtie2/2.3.5.1-GCC-8.3.0
module load HTSeq/0.11.2-foss-2019b-Python-3.7.4

#commented out is diseased plaque 
#bowtie2 -x /data/mramseylab/scripts/ALScripts/2023/newindex/smitis -q -k 1 -U /data/mramseylab/raw_reads/2014_Jorth/SRR1045151.fastq -S SRR1045151.sam
#bowtie2 -x /data/mramseylab/scripts/ALScripts/2023/newindex/smitis -q -k 1 -U /data/mramseylab/raw_reads/2014_Jorth/SRR1045152.fastq -S SRR1045152.sam
#bowtie2 -x /data/mramseylab/scripts/ALScripts/2023/newindex/smitis -q -k 1 -U /data/mramseylab/raw_reads/2014_Jorth/SRR1045153.fastq -S SRR1045153.sam
bowtie2 -x /data/mramseylab/scripts/ALScripts/2023/newindex/smitis -q -k 1 -U /data/mramseylab/raw_reads/2014_Jorth/SRR1045154.fastq -S SRR1045154.sam
bowtie2 -x /data/mramseylab/scripts/ALScripts/2023/newindex/smitis -q -k 1 -U /data/mramseylab/raw_reads/2014_Jorth/SRR1045155.fastq -S SRR1045155.sam
bowtie2 -x /data/mramseylab/scripts/ALScripts/2023/newindex/smitis -q -k 1 -U /data/mramseylab/raw_reads/2014_Jorth/SRR1045157.fastq -S SRR1045157.sam
bowtie2 -x /data/mramseylab/scripts/ALScripts/2023/newindex/smitis -q -k 1 -U /data/mramseylab/raw_reads/2014_Jorth/SRR1534916.fastq -S SRR1534916.sam
bowtie2 -x /data/mramseylab/scripts/ALScripts/2023/newindex/smitis -q -k 1 -U /data/mramseylab/raw_reads/2014_Jorth/SRR1534917.fastq -S SRR1534917.sam


#htseq-count -s yes -t CDS -a 1 -m intersection-nonempty -i ID SRR1045151.sam smitis.gff > condition2_JMT_counts1.txt
#htseq-count -s yes -t CDS -a 1 -m intersection-nonempty -i ID SRR1045152.sam smitis.gff > condition2_JMT_counts2.txt
#htseq-count -s yes -t CDS -a 1 -m intersection-nonempty -i ID SRR1045153.sam smitis.gff > condition2_JMT_counts3.txt
htseq-count -s yes -t CDS -a 1 -m intersection-nonempty -i ID SRR1045154.sam smitis.gff > condition2_JMT_counts4.txt
htseq-count -s yes -t CDS -a 1 -m intersection-nonempty -i ID SRR1045155.sam smitis.gff > condition2_JMT_counts5.txt
htseq-count -s yes -t CDS -a 1 -m intersection-nonempty -i ID SRR1045157.sam smitis.gff > condition2_JMT_counts6.txt
htseq-count -s yes -t CDS -a 1 -m intersection-nonempty -i ID SRR1534916.sam smitis.gff > condition2_JMT_counts7.txt
htseq-count -s yes -t CDS -a 1 -m intersection-nonempty -i ID SRR1534917.sam smitis.gff > condition2_JMT_counts8.txt

mkdir alignment
mv *.sam ./alignment

mkdir figures
mkdir kegg_analysis
mkdir rnaseq_analysis

Rscript deseq_tablesandkegg.R