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comparison scripts/TEMP_Insertion.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 e7d3dc3e0ec9
children
comparison
equal deleted inserted replaced
20:6e02b9179a24 21:9672fe07a232
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