This is the command genome-music-bmr-calc-wig-covgp that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
genome music bmr calc-wig-covg - Count covered bases per-gene for each given wiggle track
This document describes genome music bmr calc-wig-covg version 0.04 (2016-01-01 at
genome music bmr calc-wig-covg --roi-file=? --reference-sequence=? --wig-list=?
... music bmr calc-wig-covg \
--wig-list input_dir/wig_list \
--output-dir output_dir/ \
--reference-sequence input_dir/all_sequences.fa \
Tab-delimited list of ROIs [chr start stop gene_name] (See Description)
Path to reference sequence in FASTA format
Tab-delimited list of WIG files [sample_name wig_file] (See Description)
Directory where output files and subdirectories will be written
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.
The regions of interest (ROIs) of each gene are typically regions targeted for
sequencing or are merged exon loci (from multiple transcripts) of genes with 2-bp
flanks (splice junctions). For per-gene base counts, an overlapping base will be
counted each time it appears in an ROI of the same gene. To avoid this, be sure to
merge together overlapping ROIs of the same gene. BEDtools' mergeBed can help if used
The reference sequence in FASTA format. If a reference sequence index is not found
next to this file (a .fai file), it will be created.
Provide a file containing sample names and the wiggle track format file locations for
each. Use the tab-delimited format [sample_name wig_file] per line. Additional columns
like clinical data are allowed, but ignored. The sample_name must be the same as the
tumor sample names used in the MAF file (16th column, with the header
Specify an output directory where the following will be created/written: roi_covgs:
Subdirectory containing per-ROI covered base counts for each sample. gene_covgs:
Subdirectory containing per-gene covered base counts for each sample. total_covgs:
File containing the overall non-overlapping coverages per sample.
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