ChIP-seq Peak Finders

Possible Candidates for Use

Name Pros Cons Input Formats Output Formats Control Data? Journal PubMed ID Requirements Comments
BayesPeak 1.2.3
(November 4, 2009)
  • Appears to be less likely to return false positives
  • Returns high-confidence regions found by other methods
  • Finds narrower regions than other methods
  • Unable to find certain peaks called by other methods
  • Confusing documentation
  • BED
  • *.frame
  • RangedData object
  • R
Yes 19772557
  • R
  • Uses Bayesian approach to peak finding
CisGenome 2.0
(January 15, 2011)
  • Built-in GUI, browser available for Windows
  • Highly confusing documentation
  • High variability observed in samples from same TF
  • Built-in GUI and browser not available for Mac/Linux
  • *.aln
  • *.cod
  • *.bar
Yes 18978777
  • gcc
  • Could not access associated journal article
CSDeconv 1.02
(March 8, 2011)
  • Resolves closely spaced peaks as separate binding sites
  • Sparse, confusing documentation
  • Solexa align (*.txt)
  • *.mat
Yes 20028542
  • MATLAB, plus two toolboxes
  • Python
  • Builds on QuEST methodology
  • Recursive approach to approximate peak shape
ERANGE 3.2.1/PeakFinder
(August 10, 2010)
  • Consistent, reproducible results
  • First developed for RNA-seq, not ChIP-seq
  • No statistical estimate of false discovery rate
  • RDS
  • *.txt
Yes 18516045
  • Could not access associated journal article
FindPeaks 4.0.15
(August 18, 2010)
  • Takes strand directionality into account
  • Many options allow for greater flexibility
  • Memory usage can be controlled
  • Suitable for analyzing TF binding sites
  • Finds closely spaced peaks in regions of overlapping alignments
  • Can generate multiple UCSC-compatible output file formats
  • Accepts a diverse range of input file formats
  • Most input file type srequire pre-processing
  • The sheer number of options can be confusing
  • BED
  • Bowtie
  • Eland, Eland export
  • GFF
  • MAQ
  • BAM/SAM
  • *.peaks
  • Wiggle
  • BedGraph
  • *.png
Yes 18599518
  • Java 1.6 or over
  • None
F-Seq 1.84
(Release date unknown)
  • Strictly enforces strand directionality
  • Strict strand directionality may result in false negatives
  • BED
  • Wiggle
  • BED
  • narrowPeak
Yes 18784119
  • Java 1.5 or over
  • None
GLITR
(Release date unknown)
  • Filters out repeated start coordinates, reducing sequencing bias
  • Finds confirmed regions missed by other algorithms
  • Journal article only compares algorithms at a single site
  • Documentation somewhat confusing
  • *.align
  • *.out
  • *.regions
Yes 19553195
  • Python 2.4 or over and several modules
  • Perl 5.8.8 or over
  • None
HPeak 2.1
(October 15, 2008)
  • Capable of accepting user-defined file formats
  • Only works with human genome
  • Does not account for read orientation/strand directionality
  • Not well suited for quantifying false detection rate
  • High variability observed in samples from same TF
  • Eland
  • BED
  • Custom formats
  • BED
  • *.out
  • *.sum
  • *.seq (FASTA)
  • *.annotation.txt
  • Wiggle
Yes 20598134
  • Perl
  • None
MACS 1.4.0rc2
(February 21, 2011)
  • Accepts multiple input file formats
  • Good spatial resolution
  • Seems to find more peaks on average than other algorithms
  • Could produce more false positives
  • BED
  • Eland
  • BAM/SAM
  • Bowtie
  • MS Excel
  • BED
  • R
  • Wiggle
Yes 18798982
  • Python 2.6 or 2.7 (2.6.5 recommended)
  • One of the most popular peak finders
MM-ChIP 1.0
(Release date unknown; corresponding article published February 1, 2011)
  • Can process ChIP-seq and ChIP-chip data
  • Uses well-established MACS algorithm
  • Uses "integrative analysis" to process multiple experimental and control datasets simultaneously
  • Algorithm parameters cannot be changed (i.e. p-value threshold, etc.)
  • Documentation does not provide information about output file(s)
  • BED
  • Unknown
Yes 21284836
  • MACS
  • Python 2.5 or above
  • Actual input consists of a specially formatted text file containing the names of the data and control files, as well as the average DNA fragment lengths
PICS 1.0.6
(July 6, 2010)
  • Accounts for missing reads
  • Resolves closely spaced peaks as separate binding sites
  • Computationally intensive
  • Only accepts single-end sequence data
  • BED
  • Eland
  • MAQ
  • Bowtie
  • RangedData
  • Bed
  • Wiggle
Yes 20528864
  • R
  • None
QuEST 2.4
(October 5, 2009)
  • Consistent, reproducible results
  • Requires background control data
  • Output ready for upload to UCSC Genome Browser
  • Capable of false discovery rate analysis
  • Large memory requirements (at least 30 GB for analysis of test data)
  • Confusing output
  • Does not convert peak scores into definitive P-values
  • Solexa align
  • Eland
  • Bowtie
  • MAQ
  • QuEST align
  • *.out
  • BED
  • Wiggle
Yes 19160518
  • Perl
  • g++
  • make
  • None
SICER 1.03
(July 20, 2009)
  • Accounts for missing reads
  • Python packages may cause problems for some users
  • BED
  • Unique format
Yes 19505939
  • Python and two packages
  • None
SIPeS 2.0
(September 14, 2010)
  • Accepts paired-end read data
  • Not applicable for single-end sequence data
  • Requires very specific input file formatting
  • Documentation is incomplete
  • FASTA
  • MS Excel
Yes 20144209
  • No specific requirements mentioned
  • None
SISSRs 1.4
(November 25, 2008)
  • Takes strand directionality into account
  • Allows for control of scanning window size
  • Good spatial resolution
  • Capable of detecting asymmetrical peaks
  • High variability observed in samples from the same TF
  • Less sensitive for certain datasets
  • BED
  • Unique format
Yes 18684996
  • Perl
  • Tends to report narrow, fixed-width peaks
spp 1.10
(Release date unknown)
  • Good spatial resolution
  • Package contains WTD (Window Tag Density) and MTC (Mirror Tag Correlation) peak finding algorithms
  • Could not find manual, only a confusing tutorial
  • Journal article only discusses algorithm performance for two DNA binding proteins and one transcription factor
  • Bowtie
  • BAM
  • Eland
  • MAQ
  • Wiggle
  • broadPeak
  • narrowPeak
  • Not known if there are other formats
Yes 19029915
  • R library
  • Boost C++ library
  • Tends to report single coordinate peaks
SWEMBL 3.3.1
(March 30, 2010)
  • No specific strengths found
  • Reads must be sorted by chromosome and increasing chromosome position
  • Documentation lacks explanations of input parameters
  • BED
  • MAQ
  • Eland
  • Wiggle
  • Not known if there are other formats
Yes Unavailable
  • No specific requirements mentioned
  • Associated journal article still in preparation
"ChipSeq Peak Finder"
(Release date unknown)
  • No specific strengths found
  • Journal article does not provide analysis of algorithm performance
  • Unique format
  • Unique format
Yes 18555785
  • Perl 5 or over
  • C/C++ compiler
  • Journal article does not discuss algorithm
  • Could not find analysis of algorithm performance
T-PIC
(Release date unknown)
  • Outperforms MACS and PeakSeq at several sites
  • Manual assumes knowledge of algorithm
  • BED
  • BED
Yes 21226895
  • Perl
  • R
  • Uses peak shape to determine significance
USeq 7.6.9
(Release date unknown)
  • Capable of false discovery rate analysis
  • Analysis is complex and requires several steps
  • Unique format
  • Unique format
Yes 19061503
  • Java 1.6 or over
  • R, plus two libraries
  • None

Unlikely Candiates for Use

Name Pros Cons Input Formats Output Formats Control Data? Journal PubMed ID Requirements Comments
ANNOVAR
(Latest version released February 20, 2011)
  • Annotation database downloads can be automated
  • Requires unusual input file format
  • Unique format
  • Unique format
No 20601685
  • Perl
  • None
ChIP-Seq analysis server
  • Can produce UCSC-compatible output file
  • Easy access to several published datasets
  • Relatively simple to operate
  • Incompatible with command line usage
  • SGA
  • SGA
No Could not find associated article
  • No specific requirements mentioned
  • Web-based interface
  • Could not find associated journal article
ChIPseqR 1.4.0
(October 5, 2010)
  • No specific strengths found
  • Confusing documentation
  • Unknown
  • Unknown
No 21281468
  • R
  • Made specifically for nucleosome binding analysis
GeneTrack
  • No specific strengths found
  • Only outdated source code is freely available
  • Most recent version incompatible with command-line use
  • Main web-based interface requires user account
  • Confusing documentation
  • High variability observed in samples from the same TF
  • May produce false negatives with closely spaced peaks
  • No statistical estimate of false discovery rate
  • Unique format
  • Tabular with headers
  • BED
  • GFF
  • Wiggle
No 18388141
  • No specific requirements mentioned
  • Cannot access web-based interface without login
PeakSeq
(Release date unknown)
  • No specific strengths found
  • Confusing documentation
  • Eland
  • *.sgr
  • BED
Yes 19122651
  • Perl
  • Could not access associated journal article
Sole-Search 1.0
(Release date unknown)
  • Capable of false discovery rate analysis
  • Incompatible with command-line usage
  • Eland, Eland extended
  • tagAlign
  • *.sgr
  • GFF
Yes 19906703
  • Java
  • Web-based interface; results sent by e-mail
W-ChIPeaks
(Release date unknown; corresponding article published December 7, 2010)
  • Can produce UCSC-compatible output files
  • Relatively simple to operate
  • Capable of false discovery rate analysis
  • Command-line based equivalent (BELT) available for download
  • Accepts *.tar.gz compressed data files
  • 3 GB limit for total size of uploaded data files
  • Requires at least 10,000 tags in each file
  • Command-line version lacks certain features of the web-based interface
  • Eland, Eland extended
  • BED
  • BAM/SAM
  • GFF
  • Bowtie
  • Custom formats
  • *.txt
  • Wiggle
  • bedGraph
Yes 21138948
  • Java 6 or later
  • Web-based interface and command-line based versions available

Other sources:
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0011471
http://www.biomedcentral.com/1471-2164/10/618
www.evolutionarygenomics.com/7620/Reading/Computation_RNA-seq.pdf

Last updated: April 29, 2011