diff --git a/Adapting_new_script_for_computing_cluster.sh b/Adapting_new_script_for_computing_cluster.sh index ed687bd..99cad3d 100755 --- a/Adapting_new_script_for_computing_cluster.sh +++ b/Adapting_new_script_for_computing_cluster.sh @@ -149,9 +149,9 @@ execute() { mapFrac=$(printf "%.4f" $(echo $map / 100 | bc -l)) dedup=$(printf "%.4f" $(grep -Po 'Unknown Library.*' dedup/${id}_dedupMetric.txt | awk '{print $10}')) filtered=$(expr $(samtools view -c dedup/${id}_dedup.bam) / 2) - ripReads=$(expr $(bedtools intersect -a dedup/${id}_dedup.bam -b dedup_peaks/${id}_dedup_peaks.narrowPeak -u -ubam | samtools view -c) / 2) + ripReads=$(expr $(bedtools intersect -a dedup/${id}_dedup.bam -b dedup_peaks/${id}_peaks.narrowPeak -u -ubam | samtools view -c) / 2) FRiP=$(printf "%.4f" $(echo $fripReads / $filtered | bc -l)) - peaks=$(expr $(wc -l <"dedup_peaks/${id}_dedup_peaks.narrowPeak") - 1) + peaks=$(expr $(wc -l <"dedup_peaks/${id}_peaks.narrowPeak") - 1) echo -e "$id\t$fragments\t$filtered\t$mapFrac\t$dedup\t$FRiP\t$peaks" >> cnt_gata_qc_metrics.txt # Here I have no idea how to transfer this