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ECO 11-03-2008 12:50 AM

A brief review of recent ChIP-Seq tools literature
Seems I can't go a week without finding a paper describing a new ChIP-Seq analytical tool, so I thought it would be helpful to put together a list of a few of the most interesting papers in this area.

For those not familiar with ChIP-Seq, it involves massively parallel sequencing of nucleic acids recovered from a chromatin-immunoprecipitation (ChIP). ChIP uses an antibody to capture protein that has been previously crosslinked to DNA in its native state. Thus, ChIP-Seq allows sequencing of all DNA that a specific protein physically interacts with within the cell.

There are quite a few studies recently which describe either a software tool, and/or an analytical framework for working with this type of data. The difficulty and thus the plethora of approaches is using the read density information to "call peaks" or more precisely, statistically significant ChIP-Seq binding sites.

Recent papers I have found helpful are below, in reverse chronological order. Please accept my apologies in advance if I've missed your favorite tool.





Hopefully those are useful. I'll post up my experiences with some of these tools soon, and would love to hear yours.

Roald 11-03-2008 01:32 AM

What a great list - thanks a lot for posting!

ECO 11-04-2008 06:37 AM

Just when I think I captured them all...another one comes out!


apfejes 11-15-2008 12:45 PM

Hey ECO,

Awesome list, I can't believe how many people there are writing ChIP-Seq software, now.

At any rate, this is a great resource for people just getting into the field. (=

Can I ask that you put a link to the FindPeaks 3.2 homepage, now? I've already got pre-compiled jar files up on the web, so maybe it's time to start pointing people in that direction (=


foolishbrat 11-18-2008 02:31 AM

Hi Eco,

Great list.

BTW, do you happen to know any literature that does the error correction model of tag counts.

Nix 12-19-2008 10:53 AM

USeq chIP-seq package
Here's our publication, it's finally out:

And the project web site:

I'd like to suggest running a bake off using some simulated spike-in data until real spike-in data becomes available. This was critical for evaluating the methods used in the USeq package. Basically add simulated spikes to real input DNA sequencing data then run your favorite software to call peaks. I'm near getting together a stranded dataset that would be a good first start. Would be nice to sweeten the pot though. Maybe we could get Illumina to throw in an iPod to the winner?

dnewkirk 04-23-2009 03:18 PM

Bioconductor is in the process of developing an R package (appropriately labeled chipseq currently) which should be released in the not too distant future. A working version can be had from the developers subversion repository, but again its incomplete and may change over time. Conversion of Data objects is a little bit troublesome, but the mailing list can be browsed for tips on this.

ewilbanks 05-08-2009 05:16 PM

Hi all,

Anyone have updates to this list of programs? :D

apfejes 05-08-2009 09:01 PM

I'll be updating FindPeaks (Vancouver Short Read Analysis Package) to version 4, shortly.... is there something specific you're looking for?

ewilbanks 05-11-2009 10:25 AM

Cool! Not looking for anything in particular, just trying to make sure I've checked out the different algorithms out there :)

Chema 05-11-2009 11:36 PM


In this paper, you can find other ChIP-seq algorithm. It is implemented in R

The baisc idea was
1) Extend the reads and use the minimum number of read that overlap a a nucleotide position among both strnad. This is, the number of reads should be supported by the two strands independently. This is to avoid peaks that have a block shape.
2)Normalize data and sample regarding their covarage distribution
3)Use permutation to estimate the FDR control

ieuanclay 06-08-2009 04:07 AM

might want to add PeakSeq too:

Not earth-shattering, but i think their advice on normalising to input is really worthwhile.

ewilbanks 07-29-2009 12:44 PM

Two new ones out there:




david.lapointe 09-30-2009 06:14 AM

Is CHiPSeq from the Wold lab not available any longer. The links seem to go nowhere.

Nicolas 10-13-2009 01:24 PM


Originally Posted by david.lapointe (Post 8832)
Is CHiPSeq from the Wold lab not available any longer. The links seem to go nowhere.

Is that what you are looking for?

tujchl 10-19-2009 10:39 PM

A wonderful work!!!
thank you

alperyilmaz 11-18-2009 10:54 AM

Where can I find the results that Nix suggested earlier, same sample sequences tested with different peak finding software?

Nix 11-18-2009 11:22 AM

Here's the thread to the ChIP Seq Challenge

sameet 04-25-2010 05:09 AM

Hi All,

We recently completed first chip-seq run in our laboratory. We could find a few good peaks with MACS. What I want to do is find the distribution of the distances of all the genes that are closes to the peaks on their respective 5' and 3' end. Is there a simple way to do it. Naturally I have the genomic coordinates. If anybody has done this before, it will help most helpful else I will try to write a tool to get it done.


ewilbanks 04-26-2010 10:29 AM

You might want to check out the following tool, which has a built in "nearest gene finder".


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