Consensus peaks given multiple (>=2) replicates¶

usage: MSPC.py [-h] [-j JID] [-w WEAK] [-s STRONG] [-g GAMMA]
               [--score_cutoff SCORE_CUTOFF]
               file [file ...]

positional arguments:
  file

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:
                        MSPC_yli11_2020-04-20)
  -w WEAK, --weak WEAK  weak peak cutoff (default: 0.0001)
  -s STRONG, --strong STRONG
                        strong peak cutoff (default: 1e-08)
  -g GAMMA, --gamma GAMMA
                        combined pvalue peak cutoff (default: 1e-12)
  --score_cutoff SCORE_CUTOFF
                        combined log pvalue peak cutoff for consensus peak
                        (default: 30)

Summary¶

MSPC comparatively evaluates ChIP-seq peaks and combines the statistical significance of repeated evidences.

The output

https://github.com/Genometric/MSPC

Input¶

Narrow peak files. The format of narrow peak files is:

NAME_peaks.narrowPeak is BED6+4 format file which contains the peak locations together with peak summit, p-value, and q-value. You can load it to the UCSC genome browser. Definition of some specific columns are:

5th: integer score. It's calculated as int(-10*log10pvalue) or int(-10*log10qvalue)
7th: fold-change at peak summit
8th: -log10pvalue at peak summit
9th: -log10qvalue at peak summit
10th: relative summit position to peak start

The 8th column will be used as input pvalue to the MSPC program.

Output¶

ConsensusPeaks.sig.bed inside the {{jobID}} folder.

A consensus peak is a peak occurring in at least 2 replicates of the given replicates and it must pass the significance cutoff.

Usage¶

Copy all the narrowPeak files into your current working dir and run the following

hpcf_interactive

module load python/2.7.13

MSPC.py *.narrowPeak

Comments¶

code @ github.