A Peak-Finder MetaServer for ChIP-seq analysis

Overview Installation User Guide Results Download About


PFMS is a MetaServer application designed for analyzing ChIP-seq data. It integrates several peak-finders within a single interface. A ChIP-seq data file can be analyzed using one or more of the peak-finders listed below.
A list of the most probable binding sites (peaks) is produced based on one of the implemented peak selection methods (BED with (voting, minFP or minFN) or WIG).

A pdf version of the user manual may be obtained here.

Instead of investigating several peak-finders to get more accurate binding sites, you can use PFMS to search for peaks in your ChIP-seq data using several peak-finders in parallel with the ability to:

- obtain a list of the most probable binding sites using different combinations of the included peak-finders
- customize the included peak-finders and get the binding sites identified by any of them.
- analyse a specific chromosome or all chromosomes of a given ChIP-seq dataset.
- get the putative binding sites in UCSC standard BED or WIG format.

Currently, the following peak-finders are supported:

  • MACS v1.3.7
  • CisGenome v2.0
  • Findpeaks v3.1.9.2
  • HPeak v1.1
  • E-range v.2.1
  • SeqSite v1.0
  • SISSRs v1.4

  • Input Data Format

    In the current version of PFMS, the ChIP-seq data should be in BED 6-columns tab-separated format with the following columns:

    chrN    chrStart    chrEnd     extra1    extra2    strandSign(+/-)

    A sample of the accepted data format:
    chrN chrStart chrEnd extra1 extra2 strandSign(+/-)
    A sample of the accepted data format:
    chr1 522319 522354 0 3 -
    chr1 553256 553291 0 3 -
    chr1 699985 700020 0 3 +

    Input file of BAM and SAM formats are also supported, since PFMS internally converts them to BED using BEDTools.

    Output Files

    The peaks identified by PFMS are given in BED or WIG format based on user-given parameters. The identified peaks are stored in a file named '*_Results.bed' or '*_Results.wig'.
    In addition, results of the selected peak-finders can be obtained by adding -store_results to the command line options (Follow this user guide).