Mercurial > repos > portiahollyoak > temp

comparison 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
comparison
equal deleted inserted replaced
20:6e02b9179a24 21:9672fe07a232
114 if [[ ! -s $name.bai ]] 114 if [[ ! -s $name.bai ]]
115 then cp $BAM.bai ./ 115 then cp $BAM.bai ./
116 fi 116 fi
117 117
118 #Detect excision sites 118 #Detect excision sites
119 samtools view -XF 0x2 $name > $i.unpair.sam 119 samtools view -F 0x2 $name > $i.unpair.sam
120 awk -F "\t" '{OFS="\t"; if ($9 != 0) print $0}' $i.unpair.sam > temp1.sam 120 awk -F "\t" '{OFS="\t"; if ($9 != 0) print $0}' $i.unpair.sam > temp1.sam
121 perl $BINDIR/pickUniqIntervalPos.pl temp1.sam $INSERT > $i.unproper.uniq.interval.bed 121 perl $BINDIR/pickUniqIntervalPos.pl temp1.sam $INSERT > $i.unproper.uniq.interval.bed
122 122
123 rm temp1.sam $i.unpair.sam 123 rm temp1.sam $i.unpair.sam
124 124