Merging bigwiggle files into one bw

usage: bw_merge.py [-h] [-j JID] [-o OUTPUT]
                   (--glob GLOB | -l LIST | -f INPUT) [-g GENOME]
                   [-s CHROM_SIZE]

optional arguments:
  -h, --help            show this help message and exit
  -j JID, --jid JID     enter a job ID, which is used to make a new directory.
                        Every output will be moved into this folder. (default:
                        bw_merge_yli11_2019-10-02)
  -o OUTPUT, --output OUTPUT
                        Output Name (default: merged)
  --glob GLOB           Matching substring in the current dir (default: None)
  -l LIST, --list LIST  Input a file containing a list of bw files (default:
                        None)
  -f INPUT, --input INPUT
                        Input file names seperated by , (default: None)

Genome Info:
  -g GENOME, --genome GENOME
                        genome version: hg19, hg38, mm9, mm10. By default,
                        specifying a genome version will automatically update
                        index file, black list, chrom size and
                        effectiveGenomeSize, unless a user explicitly sets
                        those options. (default: hg19)
  -s CHROM_SIZE, --chrom_size CHROM_SIZE
                        chrome size (default: /home/yli11/Data/Human/hg19/anno
                        tations/hg19.chrom.sizes)

Summary

bigWigMerge: Merge together multiple bigWigs into a single bw file. The signal values are just added together to merge them.

Note

By default, genome is hg19.

Usage

There are 3 ways to use this program.

Example 1: Merge all bw files that match to a common string

The following code will merge all bw files that match to *CTCF*all.bw

hpcf_interactive

module load python/2.7.13

bw_merge.py --glob "*CTCF*all.bw"

Note

quotation mark here is required.

Example 2: Specify the files in a list

input.list
----------

1047946_Hudep1_CTCFIP.all.bw
1047946_Hudep1_CTCFIP.rmdup.bw
1047946_Hudep1_CTCFIP.rmdup.uq.bw

bw_merge.py -l input.list

Example 3: Specify the filenames

File names are separated by ,

bw_merge.py -f 1047946_Hudep1_CTCFIP.all.bw,1047946_Hudep1_CTCFIP.rmdup.bw

Output

The merged bw file merged.bw is located at jobID folder. You can also specify the output filename using -o option.

FAQ

Known issue: ChIP-seq IgG or input tracks can’t be merged. I don’t know why.

Comments

code @ github.