The bdgbroadcall subcommand of the MACS3 suite identifies ‘nested’ broad peaks from a single bedGraph track for scores, a function essential in certain ChIP-Seq analyses.

Detailed Description

The bdgbroadcall command takes an input bedGraph file and produces an output file with broad peaks called. It is important to note: only bedGraph files from MACS3 are acceptable to use in the bdgbroadcall command, as All regions on the same chromosome in the bedGraph file should be continuous.

Unlike narrow peak calling performed using bdgpeakcall or callpeak without the --broad option, this command, along with the --broad option in callpeak, facilitates broad peak calling, producing results in the UCSC gappedPeak format which encapsulates a nested structure of peaks. To conceptualize ‘nested’ peaks, picture a gene structure housing regions analogous to exons (strong peaks) and introns coupled with UTRs (weak peaks). The broad peak calling process utilizes two distinct cutoffs to discern broader, weaker peaks and narrower, stronger peaks, which are subsequently nested to provide a detailed peak landscape.

Please note that, if you only want to call ‘broader’ peak and not interested in the nested peak structure, please simply use bdgpeakcall with weaker cutoff.

Command Line Options

The command line options for bdgbroadcall are defined in macs3 bdgbroadcall --help command. Here is a brief overview of these options:

  • -i or --ifile: Genome-wide score for each possible location in bedGraph format. This is REQUIRED.

  • -c or --cutoff-peak: Cutoff for stronger and narrower peaks depending on which method you used for the score track. If the file contains qvalue scores from MACS3, score 2 means qvalue 0.01. DEFAULT: 2

  • -C or --cutoff-link: Cutoff for weaker and broader regions depending on which method you used for the score track. If the file contains qvalue scores from MACS3, score 1 means qvalue 0.1, and score 0.3 means qvalue 0.5. DEFAULT: 1

  • -l or --min-length: Minimum length of stronger peak, better to set it as d value. DEFAULT: 200

  • -g or --lvl1-max-gap: Maximum gap between stronger peaks, better to set it as the tag size. DEFAULT: 30

  • -G or --lvl2-max-gap: Maximum gap between weaker peaks, better to set it as 4 times the d value. DEFAULT: 800

  • --no-trackline: Tells MACS not to include a trackline with bedGraph files. The trackline is used by UCSC for display.

  • --verbose: Set verbose level of runtime messages. 0: only show critical messages, 1: show additional warning messages, 2: show process information, 3: show debug messages. DEFAULT: 2

  • --outdir: If specified, all output files will be written to that directory. Default: the current working directory

  • -o or --ofile: Output file name. Mutually exclusive with --o-prefix.

  • --o-prefix: Output file prefix. Mutually exclusive with -o/--ofile.

Example Usage

Here is an example of how to use the bdgbroadcall command:

macs3 bdgbroadcall -i input.bedGraph -o output.gappedPeak -c 2 -C 1.5 -l 500 -g 500 -G 1000

In this example, the program will call broad peaks from the input.bedGraph file and write the result to output.gappedPeak. The cutoff value for calling stronger peaks is set to 2.0, the minimum length of stronger peaks is set to 500, the maximum gap between stronger peaks is set to 500, the cutoff value for weaker peaks is set to 1.5, and the maximum gap for weaker peaks is set to 1000.