Mercurial > repos > portiahollyoak > temp
comparison scripts/TEMP_Insertion.sh @ 12:ca36262102d8 draft
planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
author | portiahollyoak |
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date | Fri, 29 Apr 2016 05:47:54 -0400 |
parents | 28d1a6f8143f |
children | e7d3dc3e0ec9 |
comparison
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11:e19d9742c99b | 12:ca36262102d8 |
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27 -t Annotated TEs in BED6 format with full path. Detected insertions that overlap with annoated TEs will be filtered. | 27 -t Annotated TEs in BED6 format with full path. Detected insertions that overlap with annoated TEs will be filtered. |
28 -u TE families annotations. If supplied detected insertions overlap with annotated TE of the same family will be filtered. Only use with -t. | 28 -u TE families annotations. If supplied detected insertions overlap with annotated TE of the same family will be filtered. Only use with -t. |
29 -m Number of mismatch allowed when mapping to TE concensus sequences. Default is 3 | 29 -m Number of mismatch allowed when mapping to TE concensus sequences. Default is 3 |
30 -x The minimum score difference between the best hit and the second best hit for considering a read as uniquely mapped. For BWA mem. | 30 -x The minimum score difference between the best hit and the second best hit for considering a read as uniquely mapped. For BWA mem. |
31 -f An integer specifying the length of the fragments (inserts) of the library. Default is 500 | 31 -f An integer specifying the length of the fragments (inserts) of the library. Default is 500 |
32 -c An integer specifying the number of CUPs used. Default is 8 | 32 -c An integer specifying the number of CPUs used. Default is 8 |
33 -h Show help message | 33 -h Show help message |
34 | 34 |
35 EOF | 35 EOF |
36 echo -en "\e[0m" | 36 echo -en "\e[0m" |
37 } | 37 } |
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 | 159 |
160 #rm $i.unpair.sam $i.unpair.uniq.bed $i.unpair.uniq.?.fastq $i.unpair.uniq.?.sai | 160 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 | 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 | 162 |
163 | 163 |
164 #Detect insertion breakpoints using soft-clipping information | 164 #Detect insertion breakpoints using soft-clipping information |
165 perl $BINDIR/pickClippedFastq.pl $i $te | 165 perl $BINDIR/pickClippedFastq.pl $i $te |
166 perl $BINDIR/refine_breakpoint.in.pl | 166 perl $BINDIR/refine_breakpoint.in.pl |
167 | 167 |
168 | 168 |
169 #Estimate insertion frequencies | 169 #Estimate insertion frequencies |
170 #if [[ $SCORE -eq 0 ]] | |
171 #then | |
170 perl $BINDIR/pickOverlapPair.in.pl $i.insertion.refined.bp $INSERT > $i.insertion.refined.bp.summary | 172 perl $BINDIR/pickOverlapPair.in.pl $i.insertion.refined.bp $INSERT > $i.insertion.refined.bp.summary |
171 | 173 #else |
174 # perl $BINDIR/pickOverlapPair.ex_MEM.pl $i.insertion.refined.bp $INSERT $SCORE > $i.insertion.refined.bp.summary | |
175 #fi | |
172 | 176 |
173 ################################ | 177 ################################ |
174 ##End of processing insertions## | 178 ##End of processing insertions## |
175 ################################ | 179 ################################ |
176 | 180 |