++ed by:

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Emmanouil "Manolis" Maragkakis
and 1 contributors


CLIPSeqTools::App::nmer_enrichment_over_shuffled - Measure Nmer enrichment over shuffled reads.


clipseqtools nmer_enrichment_over_shuffled [options/parameters]


Measure words of length N (Nmer) enrichment and compare to shuffled reads. Shuffling 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,
    --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

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

  Other options.
    --nmer_length <Int>    length N of the Nmer. Default: 6
    --permutations <Int>   number of permutation to be performed. 
                           Use more than 100 to get p-values < 0.01.
    --subset <Num>         run analysis on random subset. Option specifies
                           number (if integer) or percent (if % is used)
                           of data to be used.
    -v --verbose           print progress lines and extra information.
    -h -? --usage --help   print help message