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