#!/bin/bash
#SBATCH -t 8:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --export=NONE

module load Bowtie2/2.3.5.1-GCC-8.3.0


bowtie2 -x /data/mramseylab/genomes/hpara/hpara -q -k 1 -U /data/mramseylab/raw_reads/2014_whiteley/SRR1045151.fastq -S SRR1045151.sam
bowtie2 -x /data/mramseylab/genomes/hpara/hpara -q -k 1 -U /data/mramseylab/raw_reads/2014_whiteley/SRR1045152.fastq -S SRR1045152.sam
bowtie2 -x /data/mramseylab/genomes/hpara/hpara -q -k 1 -U /data/mramseylab/raw_reads/2014_whiteley/SRR1045153.fastq -S SRR1045153.sam
bowtie2 -x /data/mramseylab/genomes/hpara/hpara -q -k 1 -U /data/mramseylab/raw_reads/2014_whiteley/SRR1045154.fastq -S SRR1045154.sam
bowtie2 -x /data/mramseylab/genomes/hpara/hpara -q -k 1 -U /data/mramseylab/raw_reads/2014_whiteley/SRR1045155.fastq -S SRR1045155.sam
bowtie2 -x /data/mramseylab/genomes/hpara/hpara -q -k 1 -U /data/mramseylab/raw_reads/2014_whiteley/SRR1045157.fastq -S SRR1045157.sam
bowtie2 -x /data/mramseylab/genomes/hpara/hpara -q -k 1 -U /data/mramseylab/raw_reads/2014_whiteley/SRR1534916.fastq -S SRR1534916.sam
bowtie2 -x /data/mramseylab/genomes/hpara/hpara -q -k 1 -U /data/mramseylab/raw_reads/2014_whiteley/SRR1534917.fastq -S SRR1534917.sam

module load HTSeq/0.11.2-foss-2019b-Python-3.7.4

htseq-count -s yes -t CDS -a 1 -m intersection-nonempty -i ID SRR1045151.sam hpara.gff > condition2_SRR1045151_counts1.txt
htseq-count -s yes -t CDS -a 1 -m intersection-nonempty -i ID SRR1045152.sam hpara.gff > condition2_SRR1045152_counts2.txt
htseq-count -s yes -t CDS -a 1 -m intersection-nonempty -i ID SRR1045153.sam hpara.gff > condition2_SRR1045153_counts3.txt
htseq-count -s yes -t CDS -a 1 -m intersection-nonempty -i ID SRR1045154.sam hpara.gff > condition2_SRR1045154_counts4.txt
htseq-count -s yes -t CDS -a 1 -m intersection-nonempty -i ID SRR1045155.sam hpara.gff > condition2_SRR1045155_counts5.txt
htseq-count -s yes -t CDS -a 1 -m intersection-nonempty -i ID SRR1045157.sam hpara.gff > condition2_SRR1045157_counts6.txt
htseq-count -s yes -t CDS -a 1 -m intersection-nonempty -i ID SRR1534916.sam hpara.gff > condition2_SRR1534916_counts7.txt
htseq-count -s yes -t CDS -a 1 -m intersection-nonempty -i ID SRR1534917.sam hpara.gff > condition2_SRR1534917_counts8.txt