Overview
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.
Why PFMS 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:
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).
