#!/bin/bash
#SBATCH -t 12:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --export=NONE

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

bowtie2 -x /data/mramseylab/genomes/smiti/smiti /data/mramseylab/raw_reads/2014_whiteley/SRR1045154.fastq -S submeta_SAMPLES1.sam
bowtie2 -x /data/mramseylab/genomes/smiti/smiti /data/mramseylab/raw_reads/2014_whiteley/SRR1045155.fastq -S submeta_SAMPLES2.sam
bowtie2 -x /data/mramseylab/genomes/smiti/smiti /data/mramseylab/raw_reads/2014_whiteley/SRR1045157.fastq -S submeta_SAMPLES3.sam
bowtie2 -x /data/mramseylab/genomes/smiti/smiti /data/mramseylab/raw_reads/2014_whiteley/SRR1534916.fastq -S submeta_SAMPLES4.sam
bowtie2 -x /data/mramseylab/genomes/smiti/smiti /data/mramseylab/raw_reads/2014_whiteley/SRR1534917.fastq -S submeta_SAMPLES5.sam


htseq-count -s yes -t CDS -a 1 -m intersection-nonempty -i ID submeta_SAMPLES1.sam /data/mramseylab/genomes/smiti/smiti.gff > condition2_submeta_counts1.txt
htseq-count -s yes -t CDS -a 1 -m intersection-nonempty -i ID submeta_SAMPLES2.sam /data/mramseylab/genomes/smiti/smiti.gff > condition2_submeta_counts2.txt
htseq-count -s yes -t CDS -a 1 -m intersection-nonempty -i ID submeta_SAMPLES3.sam /data/mramseylab/genomes/smiti/smiti.gff > condition2_submeta_counts3.txt
htseq-count -s yes -t CDS -a 1 -m intersection-nonempty -i ID submeta_SAMPLES3.sam /data/mramseylab/genomes/smiti/smiti.gff > condition2_submeta_counts3.txt
htseq-count -s yes -t CDS -a 1 -m intersection-nonempty -i ID submeta_SAMPLES3.sam /data/mramseylab/genomes/smiti/smiti.gff > condition2_submeta_counts3.txt

mkdir alignment
mv *.sam ./alignment

mkdir figures
mkdir kegg_analysis
mkdir rnaseq_analysis

Rscript deseq_tablesandkegg.R