Mercurial > repos > portiahollyoak > temp
comparison scripts/TEMP_Insertion.sh @ 21:9672fe07a232 draft default tip
planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
author | mvdbeek |
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date | Mon, 05 Dec 2016 09:58:47 -0500 |
parents | e7d3dc3e0ec9 |
children |
comparison
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20:6e02b9179a24 | 21:9672fe07a232 |
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124 if [[ ! -s $name.bai ]] | 124 if [[ ! -s $name.bai ]] |
125 then cp $BAM.bai ./ | 125 then cp $BAM.bai ./ |
126 fi | 126 fi |
127 | 127 |
128 # Get the mate seq of the uniq-unpaired reads | 128 # Get the mate seq of the uniq-unpaired reads |
129 samtools view -XF 0x2 $name > $i.unpair.sam | 129 samtools view -F 0x2 $name > $i.unpair.sam |
130 if [[ $SCORE -eq 0 ]] | 130 if [[ $SCORE -eq 0 ]] |
131 then | 131 then |
132 perl $BINDIR/pickUniqPairFastq.pl $i.unpair.sam $i.unpair.uniq | 132 perl $BINDIR/pickUniqPairFastq.pl $i.unpair.sam $i.unpair.uniq |
133 perl $BINDIR/pickUniqPos.pl $i.unpair.sam > $i.unpair.uniq.bed | 133 perl $BINDIR/pickUniqPos.pl $i.unpair.sam > $i.unpair.uniq.bed |
134 else | 134 else |
142 bwa aln -t $CPU -n $MM -l 100 -R 1000 $te $i.unpair.uniq.2.fastq > $i.unpair.uniq.2.sai | 142 bwa aln -t $CPU -n $MM -l 100 -R 1000 $te $i.unpair.uniq.2.fastq > $i.unpair.uniq.2.sai |
143 bwa sampe -P $te $i.unpair.uniq.1.sai $i.unpair.uniq.2.sai $i.unpair.uniq.1.fastq $i.unpair.uniq.2.fastq > $i.unpair.uniq.transposons.sam | 143 bwa sampe -P $te $i.unpair.uniq.1.sai $i.unpair.uniq.2.sai $i.unpair.uniq.1.fastq $i.unpair.uniq.2.fastq > $i.unpair.uniq.transposons.sam |
144 | 144 |
145 | 145 |
146 #Summary | 146 #Summary |
147 samtools view -hSXF 0x2 $i.unpair.uniq.transposons.sam > $i.unpair.uniq.transposons.unpair.sam | 147 samtools view -hSF 0x2 $i.unpair.uniq.transposons.sam > $i.unpair.uniq.transposons.unpair.sam |
148 perl $BINDIR/pickUniqMate.pl $i.unpair.uniq.transposons.unpair.sam $i.unpair.uniq.bed > $i.unpair.uniq.transposons.bed | 148 perl $BINDIR/pickUniqMate.pl $i.unpair.uniq.transposons.unpair.sam $i.unpair.uniq.bed > $i.unpair.uniq.transposons.bed |
149 cp $i.unpair.uniq.transposons.bed $i.unpair.uniq.transposons.filtered.bed | 149 cp $i.unpair.uniq.transposons.bed $i.unpair.uniq.transposons.filtered.bed |
150 | 150 |
151 | 151 |
152 #Prepare for insertion breakpoints identification | 152 #Prepare for insertion breakpoints identification |