Postprocessing: BEDGRAPH to BW Conversion - GarrettJenkinson/informME GitHub Wiki

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]>