NAME
distribution_on_genic_elements.pl
SYNOPSIS
distribution_on_genic_elements.pl [options/parameters]
Measure the distribution of reads along idealized transcript elements. Split the 5'UTR, CDS and 3'UTR of coding transcripts in bins and measure the read density in each bin.
Input options for library.
-type <Str> input type (eg. DBIC, BED).
-file <Str> input file. Only works if type specifies a file type.
-driver <Str> driver for database connection (eg. mysql, SQLite). Only works if type is DBIC.
-database <Str> database name or path to database file for file based databases (eg. SQLite). Only works if type is DBIC.
-table <Str> database table. Only works if type is DBIC.
-host <Str> hostname for database connection. Only works if type is DBIC.
-user <Str> username for database connection. Only works if type is DBIC.
-password <Str> password for database connection. Only works if type is DBIC.
-records_class <Str> type of records stored in database (Default: GenOO::Data::DB::DBIC::Species::Schema::SampleResultBase::v3).
Other input.
-gtf <Str> GTF file for transcripts.
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.
-bins <Int> the number of bins to divide the length of each element.
-v verbosity. If used progress lines are printed.
-h print help message
-man show man pageDESCRIPTION
Measure the distribution of reads along idealized transcript elements. Divide the 5'UTR, CDS and 3'UTR of coding transcripts in bins and measure the read density in each bin.