#!/bin/bash
#SBATCH -t 48:00:00
#SBATCH --nodes=1 --ntasks-per-node=10
#SBATCH --mem=120Gb
#SBATCH --export=NONE
#SBATCH --mail-user=thpalma@uri.edu
#SBATCH --mail-type=END,FAIL


module load Bowtie2/2.3.5.1-GCC-8.3.0


bowtie2 -x /data/mramseylab/TnSeq_THP/paper_essential_genome/rnaseq/meta2/hpara -q -k 1 -U /data/mramseylab/raw_reads/2018_meta/MT48_01_R1.fastq -S MT48_01_R1.sam
bowtie2 -x /data/mramseylab/TnSeq_THP/paper_essential_genome/rnaseq/meta2/hpara -q -k 1 -U /data/mramseylab/raw_reads/2018_meta/MT48_02_R1.fastq -S MT48_02_R1.sam
bowtie2 -x /data/mramseylab/TnSeq_THP/paper_essential_genome/rnaseq/meta2/hpara -q -k 1 -U /data/mramseylab/raw_reads//2018_meta/MT48_03_R1.fastq -S MT48_03_R1.sam
bowtie2 -x /data/mramseylab/TnSeq_THP/paper_essential_genome/rnaseq/meta2/hpara -q -k 1 -U /data/mramseylab/raw_reads//2018_meta/MT48_04_R1.fastq -S MT48_04_R1.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 MT48_01_R1.sam hpara.gff > condition2_MT48_01_R1_counts1.txt
htseq-count -s yes -t CDS -a 1 -m intersection-nonempty -i ID MT48_02_R1.sam hpara.gff > condition2_MT48_02_R1_counts2.txt
htseq-count -s yes -t CDS -a 1 -m intersection-nonempty -i ID MT48_03_R1.sam hpara.gff > condition2_MT48_03_R1_counts3.txt
htseq-count -s yes -t CDS -a 1 -m intersection-nonempty -i ID MT48_04_R1.sam hpara.gff > condition2_MT48_04_R1_counts4.txt