NAME

CLIPSeqTools::App::genomic_distribution - Count reads on genes, repeats, exons, introns, 5'UTRs, ...

SYNOPSIS

clipseqtools genomic_distribution [options/parameters]

DESCRIPTION

Measure the number of reads that align to each genome wide annotation such as genic, intergenic, repeats, exonic, intronic, etc.

OPTIONS

Input options for library.
  --driver <Str>         driver for database connection (eg. mysql,
                         SQLite).
  --database <Str>       database name or path to database file for file
                         based databases (eg. SQLite).
  --table <Str>          database table.
  --host <Str>           hostname for database connection.
  --user <Str>           username for database connection.
  --password <Str>       password for database connection.
  --records_class <Str>  type of records stored in database.
  --filter <Filter>      filter library. May be used multiple times.
                         Syntax: column_name="pattern"
                         e.g. keep reads with deletions AND not repeat
                              masked AND longer than 31
                              --filter deletion="def" 
                              --filter rmsk="undef" .
                              --filter query_length=">31".
                         Operators: >, >=, <, <=, =, !=, def, undef

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

Other options.
  --plot                 call plotting script to create plots.
  -v --verbose           print progress lines and extra information.
  -h -? --usage --help   print help message