NAME
CLIPSeqTools::App::genomic_distribution - Count reads on genes, repeats, exons, introns, 5'UTRs, ...
SYNOPSIS
clipseqtools genomic_distribution [options/parameters]
DESCRIPTION
Measure the number of reads that align to each genome wide annotation such as genic, intergenic, repeats, exonic, intronic, etc.
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.
--plot call plotting script to create plots.
-v --verbose
progress lines and extra information.
-h -? --usage --help
help message