Mercurial > repos > portiahollyoak > temp

comparison scripts/TEMP_Insertion.sh @ 17:e7d3dc3e0ec9 draft

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planemo upload for repository https://github.com/portiahollyoak/Tools commit 22724a75342e3097cd0976e4bfcfe7a19308ac4f-dirty
author portiahollyoak
date Wed, 15 Jun 2016 10:30:06 -0400
parents ca36262102d8
children 9672fe07a232
comparison
equal deleted inserted replaced
16:c613f8c96e6d 17:e7d3dc3e0ec9
154 perl $BINDIR/mergeTagsWithoutGap.pl tmp > $i.uniq.transposons.filtered.woGap.bed 154 perl $BINDIR/mergeTagsWithoutGap.pl tmp > $i.uniq.transposons.filtered.woGap.bed
155 perl $BINDIR/mergeTagsWithGap.pl $i.uniq.transposons.filtered.woGap.bed $INSERT > $i.uniq.transposons.filtered.wGap.bed 155 perl $BINDIR/mergeTagsWithGap.pl $i.uniq.transposons.filtered.woGap.bed $INSERT > $i.uniq.transposons.filtered.wGap.bed
156 rm tmp 156 rm tmp
157 perl $BINDIR/get_class.pl $i.uniq.transposons.filtered.wGap.bed $i > $i.uniq.transposons.filtered.wGap.class.bed 157 perl $BINDIR/get_class.pl $i.uniq.transposons.filtered.wGap.bed $i > $i.uniq.transposons.filtered.wGap.class.bed
158 perl $BINDIR/make.bp.bed.pl $i.uniq.transposons.filtered.wGap.class.bed $ANNO $FAMI 158 perl $BINDIR/make.bp.bed.pl $i.uniq.transposons.filtered.wGap.class.bed $ANNO $FAMI
159 echo "got FAMI"
159 160
160 rm $i.unpair.sam $i.unpair.uniq.bed $i.unpair.uniq.?.fastq $i.unpair.uniq.?.sai 161 rm $i.unpair.sam $i.unpair.uniq.bed $i.unpair.uniq.?.fastq $i.unpair.uniq.?.sai
161 rm $i.unpair.uniq.transposons.sam $i.unpair.uniq.transposons.unpair.sam $i.uniq.transposons.filtered.woGap.bed $i.uniq.transposons.filtered.wGap.bed 162 rm $i.unpair.uniq.transposons.sam $i.unpair.uniq.transposons.unpair.sam $i.uniq.transposons.filtered.woGap.bed $i.uniq.transposons.filtered.wGap.bed
162 163
163 164