Mercurial > repos > portiahollyoak > temp

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
author mvdbeek
date Mon, 05 Dec 2016 09:58:47 -0500
parents e7d3dc3e0ec9
children
line wrap: on
line diff
--- a/scripts/TEMP_Insertion.sh	Wed Oct 26 07:24:45 2016 -0400
+++ b/scripts/TEMP_Insertion.sh	Mon Dec 05 09:58:47 2016 -0500
@@ -126,7 +126,7 @@
 fi
 
 # Get the mate seq of the uniq-unpaired reads
-samtools view -XF 0x2  $name > $i.unpair.sam
+samtools view -F 0x2  $name > $i.unpair.sam
 if [[ $SCORE -eq 0 ]]
 then
     perl $BINDIR/pickUniqPairFastq.pl $i.unpair.sam $i.unpair.uniq
@@ -144,7 +144,7 @@
 
 
 #Summary
-samtools view -hSXF 0x2 $i.unpair.uniq.transposons.sam > $i.unpair.uniq.transposons.unpair.sam
+samtools view -hSF 0x2 $i.unpair.uniq.transposons.sam > $i.unpair.uniq.transposons.unpair.sam
 perl $BINDIR/pickUniqMate.pl $i.unpair.uniq.transposons.unpair.sam $i.unpair.uniq.bed > $i.unpair.uniq.transposons.bed
 cp $i.unpair.uniq.transposons.bed $i.unpair.uniq.transposons.filtered.bed