NAME

CLIPSeqTools::PreprocessApp::star_alignment - Do reads alignment with STAR.

SYNOPSIS

clipseqtools-preprocess star_alignment [options/parameters]

DESCRIPTION

Do reads alignment with STAR.

OPTIONS

  Input.
    --fastq <Str>          FastQ file with the reads.
    --star_genome <Str>    directory with STAR genome index

  Output
    --o_prefix <Str>       output path prefix. Script will create and add
                           extension to path. [Default: ./]

  Other options.
    --star_path <Str>      path to STAR executable. [Default: STAR].
    --threads <Int>        number of threads to use. [Default: 4].
    -v --verbose           print progress lines and extra information.
    -h -? --usage --help   print help message