-
Notifications
You must be signed in to change notification settings - Fork 8
Postprocessing: BEDGRAPH to BW Conversion
The user can employ a provided utility to convert BED files generated by informME to much smaller BigWig (BW) files. This can be done by running the command:
bed2bw.sh BED_DIR GENOME
where
-
BED_DIR
is the path containing the BED files -
GENOME
is the assembly of the reference genome used to generate the BED files (e.g.,GENOME
must be set to "hg19" when the Human assembly hg19 is used)
NOTE 1: For this utility, the following tools must be installed in $PATH
: bedtools, bedClip, bedGraphToBigWig, and fetchChromSizes
NOTE 2: Here is the full help file for bed2bw.sh
:
Description:
Convert all BED files in input directory into bigWig files.
Usage:
bed2bw.sh [OPTIONS] BED_DIR GENOME
Options:
-h|--help Help.
-d|--outdir Output directory. Default: $PWD.
Examples:
bed2bw.sh -d out input_bed_files/ hg19
Output:
A .bw file for each BED file.
Dependancies:
fetchChromSizes
bedtools
bedClip
bedGraphToBigWig
Upstream:
singleMethAnalysisToBed.sh or makeBedsForDiffMethAnalysis.sh.
Authors:
Garrett Jenkinson <[email protected]>
Jordi Abante <[email protected]>
If you use informME, please cite:
[1] Jenkinson, G., Pujadas, E., Goutsias, J., and Feinberg, A.P. (2017), Potential energy landscapes identify the information-theoretic nature of the epigenome, Nature Genetics, 49: 719-729.
[2] Jenkinson, G., Abante, J., Feinberg, A.P., and Goutsias, J. (2018), An information-theoretic approach to the modeling and analysis of whole-genome bisulfite sequencing data, BMC Bioinformatics, 19:87, https://doi.org/10.1186/s12859-018-2086-5.
[3] Jenkinson, G., Abante, J., Koldobskiy, M., Feinberg, A.P., and Goutsias, J. (2019), Ranking genomic features using an information-theoretic measure of epigenetic discordance, BMC Bioinformatics, 20:175, https://doi.org/10.1186/s12859-019-2777-6.
- Home
- Software Overview
- Dependencies
- Installing InformME
- Directory Structure
- Usage
- Reference Genome Analysis
- Methylation Data Matrix Generation
- Model Estimation & Analysis
- Generate BEDGRAPH Files for Single Analysis
- Generate BEDGRAPH Files for Differential Analysis
- Postprocessing: BEDGRAPH to BW Conversion
- Postprocessing: DMR Detection
- Postprocessing: Gene Ranking
- Testing/Debugging Your Install
- FAQs
- Version History
- Licencing