Mercurial > repos > portiahollyoak > temp

diff scripts/TEMP_Absence.sh @ 21:9672fe07a232 draft default tip

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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
author mvdbeek
date Mon, 05 Dec 2016 09:58:47 -0500
parents ca36262102d8
children
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--- a/scripts/TEMP_Absence.sh	Wed Oct 26 07:24:45 2016 -0400
+++ b/scripts/TEMP_Absence.sh	Mon Dec 05 09:58:47 2016 -0500
@@ -116,7 +116,7 @@
 fi
 
 #Detect excision sites
-samtools view -XF 0x2 $name > $i.unpair.sam
+samtools view -F 0x2 $name > $i.unpair.sam
 awk -F "\t" '{OFS="\t"; if ($9 != 0) print $0}' $i.unpair.sam > temp1.sam
 perl $BINDIR/pickUniqIntervalPos.pl temp1.sam $INSERT > $i.unproper.uniq.interval.bed