#!/bin/bash
#SBATCH --time=60:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=64
#SBATCH --mem=20000
#SBATCH --partition=amd
#run rseqc script

#make a directory for rseqc output
#mkdir ./rseqc
#load conda
module load conda
#activate virtual enviroment
source activate py3venv
#run rseqc geneBody_coverage
geneBody_coverage.py -r /scratch/cmp1g20/ref_genome/hg38.HouseKeepingGenes.bed  -i /scratch/cmp1g20/Neuroblastoma_RNAseq/All_bam_files -o /scratch/cmp1g20/Neuroblastoma_RNAseq/rseqc

