NAME
CLIPSeqTools::App::cluster_size_and_score_distribution - Assemble reads in clusters and measure their size and number of contained reads distribution
SYNOPSIS
clipseqtools cluster_size_and_score_distribution [options/parameters]
DESCRIPTION
Assemble reads in clusters and measure their size and number of contained reads distribution. Reads that are closer than a user defined threshold are assembled in clusters. Cluster size and number of reads (score) contained in each cluster is measured. Output: Distribution of cluster size (cluster_size_distribution.tab). Distribution of cluster scores (cluster_score_distribution.tab).
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.
--allowed_dis <Int> reads closer than this value are assembled in
clusters. Default: 0
--plot call plotting script to create plots.
-v --verbose print progress lines and extra information.
-h -? --usage --help print help message