From e1cc50f4fb1afbd6acab7ee0dd43149c51421362 Mon Sep 17 00:00:00 2001
From: Donald Buczek <buczek@molgen.mpg.de>
Date: Tue, 13 Sep 2022 14:30:43 +0200
Subject: [PATCH] Fix dedup/${id}_peaks.narrowPeak filename
---
Adapting_new_script_for_computing_cluster.sh | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/Adapting_new_script_for_computing_cluster.sh b/Adapting_new_script_for_computing_cluster.sh
index ed687bd..99cad3d 100755
--- a/Adapting_new_script_for_computing_cluster.sh
+++ b/Adapting_new_script_for_computing_cluster.sh
@@ -149,9 +149,9 @@ execute() {
mapFrac=$(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