#!/bin/bash
#SBATCH -t 6:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --export=NONE
./cmatrichmonoRNAscript.sh

module load bowtie2/2.2.9-foss-2016b
module load HTSeq/0.8.0-foss-2016b-Python-2.7.12

bowtie2 -x ~/genomes/cmatcanu -1 cmana1_R1.fastq -2 cmana1_R2.fastq -S cmatrichana-1.sam -p 2
bowtie2 -x ~/genomes/cmatcanu -1 cmana2_R1.fastq -2 cmana2_R2.fastq -S cmatrichana-2.sam -p 2
bowtie2 -x ~/genomes/cmatcanu -1 cmscri1_R1.fastq -2 cmscri1_R2.fastq -S cmatanascri-1.sam -p 2
bowtie2 -x ~/genomes/cmatcanu -1 cmscri2_R1.fastq -2 cmscri2_R2.fastq -S cmatanascri-2.sam -p 2
bowtie2 -x ~/genomes/cmatcanu -1 cmsmit1_R1.fastq -2 cmsmit1_R2.fastq -S cmatanasmit-1.sam -p 2
bowtie2 -x ~/genomes/cmatcanu -1 cmsmit2_R1.fastq -2 cmsmit2_R2.fastq -S cmatanasmit-2.sam -p 2

htseq-count -s reverse -t CDS -a 1 -m intersection-nonempty -i ID cmatrichana-1.sam ~/genomes/cmat_rast.gff > cmatanamono-1.count.txt
htseq-count -s reverse -t CDS -a 1 -m intersection-nonempty -i ID cmatrichana-2.sam ~/genomes/cmat_rast.gff > cmatanamono-2.count.txt
htseq-count -s reverse -t CDS -a 1 -m intersection-nonempty -i ID cmatanascri-1.sam ~/genomes/cmat_rast.gff > cmatanascri-1.count.txt
htseq-count -s no -t CDS -a 1 -m intersection-nonempty -i ID cmatanascri-2.sam ~/genomes/cmat_rast.gff > cmatanascri-2.count.txt
htseq-count -s no -t CDS -a 1 -m intersection-nonempty -i ID cmatanasmit-1.sam ~/genomes/cmat_rast.gff > cmatanasmit-1.count.txt
htseq-count -s no -t CDS -a 1 -m intersection-nonempty -i ID cmatanasmit-2.sam ~/genomes/cmat_rast.gff > cmatanasmit-2.count.txt