From 1fe7064abfebfa257622cbd14e12d4dba64a6f31 Mon Sep 17 00:00:00 2001
From: Donald Buczek <buczek@molgen.mpg.de>
Date: Wed, 14 Sep 2022 07:43:28 +0200
Subject: [PATCH] Fix fripReads
---
Adapting_new_script_for_computing_cluster.sh | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Adapting_new_script_for_computing_cluster.sh b/Adapting_new_script_for_computing_cluster.sh
index 718f6a3..0cc30a6 100755
--- a/Adapting_new_script_for_computing_cluster.sh
+++ b/Adapting_new_script_for_computing_cluster.sh
@@ -149,7 +149,7 @@ 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/${id}_peaks.narrowPeak -u -ubam | samtools view -c) / 2)
+ fripReads=$(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}_peaks.narrowPeak") - 1)
echo -e "$id\t$fragments\t$filtered\t$mapFrac\t$dedup\t$FRiP\t$peaks" >> cnt_gata_qc_metrics.txt