CLIPSeqTools::App::cluster_size_and_score_distribution - Assemble reads in clusters and measure their size and number of contained reads distribution
clipseqtools cluster_size_and_score_distribution [options/parameters]
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).
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