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 0.04 (2018-07-05 at 09:17:13)

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¶

--roi-file

--reference-sequence

--wig-list

--output-dir

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)