4 The `cmbreps` command is part of the MACS3 suite of tools and is used
5 to combine bedGraph files from replicates. It is particularly useful
6 in ChIP-Seq analysis where multiple replicates of the same experiment
9 ## Detailed Description
11 The `cmbreps` command takes a list of input bedGraph files
12 (replicates) and produces an output file with combined scores. Note:
13 All regions on the same chromosome in the bedGraph file should be
14 continuous so bedGraph files from MACS3 are recommended.
16 The `cmbreps` command provides different way to combine replicates,
17 compared with the `callpeak` command where all replicates will be
18 simply pooled. A possible usage is that: for each replicate, we can
19 first follow the instructions in the [Advanced Step-by-step Peak
20 Calling](./Advanced_Step-by-step_Peak_Calling.md) to generate the
21 p-value scores through `bdgcmp -m ppois`, use `cmbreps -m fisher` to
22 use Fisher's combined probability test to combine all the p-value
23 score tracks and generate a single BedGraph, then call peaks using
26 ## Command Line Options
28 Here is a brief overview of command line options:
30 - `-i IFILE1 IFILE2 [IFILE3 ...]`: MACS score in bedGraph for each
31 replicate. Require at least 2 files. REQUIRED
32 - `-m` or `--method`: Method to use while combining scores from
34 - `fisher`: Fisher's combined probability test. It requires scores
35 in ppois form (-log10 pvalues) from `bdgcmp`. Other types of
36 scores for this method may cause cmbreps unexpected errors.
37 - `max`: Take the maximum value from replicates for each genomic
39 - `mean`: Take the average value. Note, except for Fisher's method,
40 max or mean will take scores AS IS which means they won't convert
41 scores from log scale to linear scale or vice versa.
42 - `--outdir`: If specified, all output files will be written to that
43 directory. Default: the current working directory
44 - `-o` or `--ofile`: Output BEDGraph filename for combined scores.
45 - `--verbose`: Set the verbose level of runtime messages. 0: only show
46 critical messages, 1: show additional warning messages, 2: show
47 process information, 3: show debug messages. DEFAULT: 2
52 Here is an example of how to use the `cmbreps` command:
55 macs3 cmbreps -i replicate1.bedGraph replicate2.bedGraph replicate3.bedGraph -o combined.bedGraph --method mean
58 In this example, the program will combine the scores in the
59 `replicate1.bedGraph`, `replicate2.bedGraph`, and
60 `replicate3.bedGraph` files and write the result to
61 `combined.bedGraph`. The method used for combining scores is `mean` so
62 it will take the average score from the three replicates at each