comparison scripts/TEMP_Insertion.sh @ 12:ca36262102d8 draft

planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50

11:e19d9742c99b

        -t     Annotated TEs in BED6 format with full path. Detected insertions that overlap with annoated TEs will be filtered. 
        -u     TE families annotations. If supplied detected insertions overlap with annotated TE of the same family will be filtered. Only use with -t.
        -m     Number of mismatch allowed when mapping to TE concensus sequences. Default is 3
        -x     The minimum score difference between the best hit and the second best hit for considering a read as uniquely mapped. For BWA mem. 
        -f     An integer specifying the length of the fragments (inserts) of the library. Default is 500
        -c     An integer specifying the number of CUPs used. Default is 8
        -h     Show help message

EOF
echo -en "\e[0m"
}

perl $BINDIR/mergeTagsWithGap.pl $i.uniq.transposons.filtered.woGap.bed $INSERT > $i.uniq.transposons.filtered.wGap.bed
rm tmp
perl $BINDIR/get_class.pl $i.uniq.transposons.filtered.wGap.bed $i > $i.uniq.transposons.filtered.wGap.class.bed
perl $BINDIR/make.bp.bed.pl $i.uniq.transposons.filtered.wGap.class.bed $ANNO $FAMI

#rm $i.unpair.sam $i.unpair.uniq.bed $i.unpair.uniq.?.fastq $i.unpair.uniq.?.sai 
rm $i.unpair.uniq.transposons.sam $i.unpair.uniq.transposons.unpair.sam $i.uniq.transposons.filtered.woGap.bed $i.uniq.transposons.filtered.wGap.bed


#Detect insertion breakpoints using soft-clipping information
perl $BINDIR/pickClippedFastq.pl $i $te
perl $BINDIR/refine_breakpoint.in.pl


#Estimate insertion frequencies
perl $BINDIR/pickOverlapPair.in.pl $i.insertion.refined.bp $INSERT > $i.insertion.refined.bp.summary


################################
##End of processing insertions##
################################

12:ca36262102d8

        -t     Annotated TEs in BED6 format with full path. Detected insertions that overlap with annoated TEs will be filtered. 
        -u     TE families annotations. If supplied detected insertions overlap with annotated TE of the same family will be filtered. Only use with -t.
        -m     Number of mismatch allowed when mapping to TE concensus sequences. Default is 3
        -x     The minimum score difference between the best hit and the second best hit for considering a read as uniquely mapped. For BWA mem. 
        -f     An integer specifying the length of the fragments (inserts) of the library. Default is 500
        -c     An integer specifying the number of CPUs used. Default is 8
        -h     Show help message

EOF
echo -en "\e[0m"
}

perl $BINDIR/mergeTagsWithGap.pl $i.uniq.transposons.filtered.woGap.bed $INSERT > $i.uniq.transposons.filtered.wGap.bed
rm tmp
perl $BINDIR/get_class.pl $i.uniq.transposons.filtered.wGap.bed $i > $i.uniq.transposons.filtered.wGap.class.bed
perl $BINDIR/make.bp.bed.pl $i.uniq.transposons.filtered.wGap.class.bed $ANNO $FAMI

rm $i.unpair.sam $i.unpair.uniq.bed $i.unpair.uniq.?.fastq $i.unpair.uniq.?.sai 
rm $i.unpair.uniq.transposons.sam $i.unpair.uniq.transposons.unpair.sam $i.uniq.transposons.filtered.woGap.bed $i.uniq.transposons.filtered.wGap.bed


#Detect insertion breakpoints using soft-clipping information
perl $BINDIR/pickClippedFastq.pl $i $te
perl $BINDIR/refine_breakpoint.in.pl


#Estimate insertion frequencies
#if [[ $SCORE -eq 0 ]]
#then
perl $BINDIR/pickOverlapPair.in.pl $i.insertion.refined.bp $INSERT > $i.insertion.refined.bp.summary
#else
#    perl $BINDIR/pickOverlapPair.ex_MEM.pl $i.insertion.refined.bp $INSERT $SCORE > $i.insertion.refined.bp.summary    
#fi

################################
##End of processing insertions##
################################