Revision 15df015227a05ce566fff158d312bd1a666e1235 authored by Anthony Findley on 29 January 2021, 16:25:53 UTC, committed by GitHub on 29 January 2021, 16:25:53 UTC
1 parent 8fd774c
coverageBed_2.25.0.sh
#!/bin/bash
#PBS -l nodes=1:ppn=1,mem=100gb
#PBS -l walltime=4:00:00
module load bedtools/2.25.0
cd $PBS_O_WORKDIR
bedtranscript=/wsu/home/groups/piquelab/data/RefTranscriptome/Sorted_NoChr_ensGene.hg19.2014.bed.gz
dataFolder=/wsu/home/fx/fx78/fx7820/rprdata/Anthony/GxE_iPSC/Shallow/${Plate}/Bam
# mygenomefile.txt is a 2-column, tab separated file containing the chromosome names and number of bp
bedtools coverage -counts -sorted -split -s -a ${bedtranscript} \
-b ${dataFolder}/${Sample}_clean.bam -g mygenomefile.txt | gzip > \
GeneCounts/${Sample}_counts.bed.gz
echo ${Sample} >> Finished.txt
Computing file changes ...
