++ed by:
ZMUGHAL

1 PAUSE user(s)

Emmanouil "Manolis" Maragkakis
and 1 contributors

NAME

CLIPSeqTools::CompareApp::libraries_relative_read_density - Measure read density around the reads of a reference library

SYNOPSIS

clipseqtools-compare libraries_relative_read_density [options/parameters]

DESCRIPTION

For a library A and a reference library B, measure the density of A reads around the middle position of B reads.

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

  Input options for reference library.
    --r_driver <Str>        driver for database connection (eg. mysql,
                            SQLite).
    --r_database <Str>      database name or path to database file for
                            file based databases (eg. SQLite).
    --r_table <Str>         database table.
    --r_host <Str>          hostname for database connection.
    --r_user <Str>          username for database connection.
    --r_password <Str>      password for database connection.
    --r_records_class <Str> type of records stored in database.
    --r_filter <Filter>     same as filter but for reference library.

  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.
    --span <Int>           the region around reference reads where density
                           is measured. [Default: 25]
    --plot                 call plotting script to create plots.
    -v --verbose           print progress lines and extra information.
    -h -? --usage --help   print help message