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
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.
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
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
--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
--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
Here is an example of how to use the
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
replicate3.bedGraph files and write the result to
combined.bedGraph. The method used for combining scores is
it will take the average score from the three replicates at each