CLIPSeqTools::PreprocessApp::cleanup_alignment - Keep a single record for multimappers, sort and collapse similar STAR alignments.
clipseqtools-preprocess cleanup_alignment [options/parameters]
Clean up STAR aligner SAM output file. Will keep only a single record for multimappers. Will sort STAR alignments and collapse alignments with same sequence and position. Will add an XC:i tag for each alignment with the copy number - the number of collapsed alignments.
Input. --sam <Str> SAM file with STAR alignments. Output --o_prefix <Str> output path prefix. Script will create and add extension to path. [Default: ./] Other options. -v --verbose print progress lines and extra information. -h -? --usage --help print help message
To install CLIPSeqTools, copy and paste the appropriate command in to your terminal.
cpanm
cpanm CLIPSeqTools
CPAN shell
perl -MCPAN -e shell install CLIPSeqTools
For more information on module installation, please visit the detailed CPAN module installation guide.