++ed by:
ZMUGHAL

1 PAUSE user

Emmanouil "Manolis" Maragkakis
and 1 contributors

NAME

CLIPSeqTools::PreprocessApp::cut_adaptor - Cut the adaptor sequence from the 3'end of reads.

SYNOPSIS

clipseqtools-preprocess cut_adaptor [options/parameters]

DESCRIPTION

Cut the adaptor sequence from the 3'end of reads. Uses cutadapt to remove the adaptor which is usually ligated at the 3'end of reads.

OPTIONS

  Input.
    --fastq <Str>          FastQ file with the reads.
    --adaptor <Str>        adaptor sequence.

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

  Other options.
    --cutadapt_path <Str>  path to cutadapt executable. [Default: cutadapt].
    -v --verbose           print progress lines and extra information.
    -h -? --usage --help   print help message