
genome music bmr calc-wig-covg
NAME
genome music bmr calc-wig-covg - Count covered bases per-gene for each given wiggle track format file.
VERSION
This document describes genome music bmr calc-wig-covg version 0.0401 (2014-02-13 at 08:01:08)
SYNOPSIS
genome music bmr calc-wig-covg --roi-file=? --reference-sequence=? --wig-list=? --output-dir=?
General usage:
... music bmr calc-wig-covg \ --wig-list input_dir/wig_list \ --output-dir output_dir/ \ --reference-sequence input_dir/all_sequences.fa \ --roi-file input_dir/all_coding_exons.tsv
REQUIRED ARGUMENTS
- roi-file Text
-
Tab-delimited list of ROIs [chr start stop gene_name] (See Description)
- reference-sequence Text
-
Path to reference sequence in FASTA format
- wig-list Text
-
Tab-delimited list of WIG files [sample_name wig_file] (See Description)
- output-dir Text
-
Directory where output files and subdirectories will be written
DESCRIPTION
This script counts bases with sufficient coverage in the ROIs of each gene from given wiggle track format files, and categorizes them into - AT, CG (non-CpG), and CpG counts. It also adds up these base-counts across all ROIs of each gene for each sample, but covered bases that lie within overlapping ROIs are not counted more than once towards these total counts.
ARGUMENTS
LICENSE
Copyright (C) 2010-2011 Washington University in St. Louis.
It is released under the Lesser GNU Public License (LGPL) version 3. See the associated LICENSE file in this distribution.
AUTHORS
Cyriac Kandoth, Ph.D.
SEE ALSO
genome-music-bmr(1), genome-music(1), genome(1)