5_Count.sh

#!/bin/bash

#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=4G
#SBATCH --job-name=read_count
#SBATCH --time=15:00:00
#SBATCH --mail-user=maelle.wannier@unifr.ch
#SBATCH --mail-type=begin,end,fail
#SBATCH --output=/home/mwannier/output_%j.o
#SBATCH --error=/home/mwannier/error_%j.e


module add UHTS/Analysis/subread/2.0.1; ##Add subread module v2.0.1 with featureCounts in it

featureCounts -a ../Mapping/reference_genome/Homo_sapiens.GRCh38.104.gtf -o ./read_count ../Mapping/outMap/*_sorted.bam ## launch featureCounts on the files in outMap(bam files sorted on last step) with the annotation file (gtf) as argument and print the output in read_count file

cut -f 1,7-12 ./read_count | tail -n +2 > ./cut_read_count ## cut the resulting file to keep only the column with the gene_ID and the counts per sample and remove the first row (empty line)