NAME

nmer_enrichment_over_shuffled.pl

SYNOPSIS

nmer_enrichment_over_shuffled.pl [options/parameters]

Measure Nmer enrichment over shuffled reads. Suffling is done at the nucleotide level and p-values are calculated using permutations.

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.
    -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 (Default: GenOO::Data::DB::DBIC::Species::Schema::SampleResultBase::v3).

Output.
    -o_file <Str>          filename for output file. If path does not exist it will be created.

Input Filters (only for DBIC input type).
    -filter <Filter>       filter library. Option can be given multiple times.
                           Filter syntax: column_name="pattern"
                             e.g. -filter deletion="def" -filter rmsk="undef" to keep reads with deletions and not repeat masked.
                             e.g. -filter query_length=">31" -filter query_length="<=50" to keep reads longer than 31 and shorter or   equal to 50.
                           Supported operators: ">", ">=", "<", "<=", "=", "!=","def", "undef"

Other options.
    -N <Int>               the length N of the Nmer. Default: 6
    -P <Int>               the number of permutation to be performed. Consider using more than 100 to get p-values < 0.01
    -sub_size <Int>        if set it specifies the number of records on which the analysis will run. Records are selected randomly.
    -sub_percent <Float>   specifies the percent of records on which the analysis will run. Records are selected randomly. Default: 100
    -v                     verbosity. If used progress lines are printed.
    -h                     print help message
    -man                   show man page

DESCRIPTION

Measure Nmer enrichment over shuffled reads. Suffling is done at the nucleotide level and p-values are calculated using permutations.