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Call Example

// on Windows
MSPC -i rep1.bed -i rep2.bed -i rep3.bed -r biological -s 1E-8 -w 1E-4

//on Linux/Mac
mono MSPC -i rep1.bed -i rep2.bed -i rep3.bed -r biological -s 1E-8 -w 1E-4


  • Microsoft Windows users: Update to .NET 4.5 or later.
  • Mac and Linux users: Download and install Mono and remember to invoke it before our MSPC command.


A BED file for each replicate, containing enriched regions (i.e. peaks) called with a permissive p-value threshold. The columns of the BED files should comply the field order defined on Ensembl: (1) chrom, (2) chromStart, (3) chromEnd, (4) name, and (5) score (p-value). The p-value needs to be in -Log10(p-value) format. More columns can be present, but they are not considered.


MSPC outputs different classifications of peaks (e.g., stringent, weak, stringent-confirmed, weak-discarded) into merged and separated BED files. An output BED file contains all parsed information of a peak (i.e., chr, chromStart, chromEnd, name, and p-value) plus the combined significance and corresponding right-tail probability. An example is as follows:

from input:
chr1 32600 32680 MACS_peak_4 4.08

in the output:
chr1 32600 32680 MACS_peak_4 4.08 222.936 46.373


You may consider following table for quick start, a detailed description of arguments are available at this page.

Argument Type short argument long argument valid values default value
Input Required -i -input BED file none
Replicate Type Required -r -replicate Bio, Biological, Tec, Technical none
Stringency threshold Required -s -tauS Double none
Weak threshold Required -w -tauW Double none
Gamma (combined stringency threshold) Optional -g -gamma Double Stringency threshold
C (minimum required overlapping peaks) Optional -c none Integer 1
Alpha (BH multiple testing correction threshold) Optional -a -alpha Double 0.05


Last edited Jul 20, 2015 at 1:58 AM by VahidJalili, version 8