#!/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


bowtie2 -x /data/mramseylab/scripts/ALScripts/sm_BP2014/newindex/smitis -q -k 1 -U /data/mramseylab/raw_reads/2018_Benitez_Paez/MT48_01_R1.fastq -S MT48_01_R1.sam
bowtie2 -x /data/mramseylab/scripts/ALScripts/sm_BP2014/newindex/smitis -q -k 1 -U /data/mramseylab/raw_reads/2018_Benitez_Paez/MT48_02_R1.fastq -S MT48_02_R1.sam
bowtie2 -x /data/mramseylab/scripts/ALScripts/sm_BP2014/newindex/smitis -q -k 1 -U /data/mramseylab/raw_reads/2018_Benitez_Paez/MT48_03_R1.fastq -S MT48_03_R1.sam
bowtie2 -x /data/mramseylab/scripts/ALScripts/sm_BP2014/newindex/smitis -q -k 1 -U /data/mramseylab/raw_reads/2018_Benitez_Paez/MT48_04_R1.fastq -S MT48_04_R1.sam


htseq-count -s yes -t CDS -a 1 -m intersection-nonempty -i ID MT48_01_R1.sam smitis.gff > condition2_MT48_counts1.txt
htseq-count -s yes -t CDS -a 1 -m intersection-nonempty -i ID MT48_02_R1.sam smitis.gff > condition2_MT48_counts2.txt
htseq-count -s yes -t CDS -a 1 -m intersection-nonempty -i ID MT48_03_R1.sam smitis.gff > condition2_MT48_counts3.txt
htseq-count -s yes -t CDS -a 1 -m intersection-nonempty -i ID MT48_04_R1.sam smitis.gff > condition2_MT48_counts4.txt

mv *.bam ./alignment

mkdir figures
mkdir kegg_analysis
mkdir rnaseq_analysis

Rscript deseq_tablesandkegg.R