From d883b42a829a0a1ae5fd5a4cc680efd426f1fb66 Mon Sep 17 00:00:00 2001
From: Holger Brandl <holgerbrandl@gmail.com>
Date: Tue, 8 Sep 2015 13:19:52 +0200
Subject: [PATCH] continued STAR evaluation
---
dge_workflow/dge_utils.sh | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/dge_workflow/dge_utils.sh b/dge_workflow/dge_utils.sh
index 16e697d..8ce498c 100755
--- a/dge_workflow/dge_utils.sh
+++ b/dge_workflow/dge_utils.sh
@@ -231,7 +231,7 @@ fi
for bamFile in $bamFiles; do
sample=$(basename $bamFile .bam)
echo "converting $bamFile to bigwig format"
- mysub "${project}__bw__${sample}" "genomeCoverageBed -bg -ibam $bamFile -g ${genomeFai} | wigToBigWig -clip stdin ${genomeFai} ${sample}.bw" -q short | joblist .bigwig
+ mysub "${project}__bw__${sample}" "genomeCoverageBed -split -bg -ibam $bamFile -g ${genomeFai} | wigToBigWig -clip stdin ${genomeFai} ${sample}.bw" -q short | joblist .bigwig
done
wait4jobs .bigwig
--
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