The cmbreps command is part of the MACS3 suite of tools and is used to combine bedGraph files from replicates. It is particularly useful in ChIP-Seq analysis where multiple replicates of the same experiment are performed.

Detailed Description

The cmbreps command takes a list of input bedGraph files (replicates) and produces an output file with combined scores. Note: All regions on the same chromosome in the bedGraph file should be continuous so bedGraph files from MACS3 are recommended.

The cmbreps command provides different way to combine replicates, compared with the callpeak command where all replicates will be simply pooled. A possible usage is that: for each replicate, we can first follow the instructions in the Advanced Step-by-step Peak Calling to generate the p-value scores through bdgcmp -m ppois, use cmbreps -m fisher to use Fisher’s combined probability test to combine all the p-value score tracks and generate a single BedGraph, then call peaks using bdgpeakcall.

Command Line Options

Here is a brief overview of command line options:

  • -i IFILE1 IFILE2 [IFILE3 ...]: MACS score in bedGraph for each replicate. Require at least 2 files. REQUIRED

  • -m or --method: Method to use while combining scores from replicates.

    • fisher: Fisher’s combined probability test. It requires scores in ppois form (-log10 pvalues) from bdgcmp. Other types of scores for this method may cause cmbreps unexpected errors.

    • max: Take the maximum value from replicates for each genomic position.

    • mean: Take the average value. Note, except for Fisher’s method, max or mean will take scores AS IS which means they won’t convert scores from log scale to linear scale or vice versa.

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

  • -o or --ofile: Output BEDGraph filename for combined scores.

  • --verbose: Set the 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

Example Usage

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

macs3 cmbreps -i replicate1.bedGraph replicate2.bedGraph replicate3.bedGraph -o combined.bedGraph --method mean

In this example, the program will combine the scores in the replicate1.bedGraph, replicate2.bedGraph, and replicate3.bedGraph files and write the result to combined.bedGraph. The method used for combining scores is mean so it will take the average score from the three replicates at each genomic location.