#!/bin/bash
#SBATCH -t 4:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --export=NONE

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 submeta_SAMPLES1.sam /data/mramseylab/genomes/cmatr/cmatr.gff > condition2_submeta_counts1.txt