Emmanouil "Manolis" Maragkakis > CLIPSeqTools-0.1.1 > CLIPSeqTools::App::genome_coverage

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Module Version: 0.1.1   Source  

NAME ^

CLIPSeqTools::App::genome_coverage - Measure percent of genome covered by reads.

SYNOPSIS ^

clipseqtools genome_coverage [options/parameters]

DESCRIPTION ^

Measure the percent of genome that is covered by the reads of a library.

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

  Other input.
    --rname_sizes <Str>    file with sizes for reference alignment
                           sequences (rnames). Must be tab delimited
                           (chromosome\tsize) with one line per rname.

  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
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