NAME

CLIPSeqTools::PreprocessApp::cleanup_alignment - Keep a single record for multimappers, sort and collapse similar STAR alignments.

SYNOPSIS

clipseqtools-preprocess cleanup_alignment [options/parameters]

DESCRIPTION

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.

OPTIONS

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