Question: Which Chip Seq Peak Callers Do You Use?
11
gravatar for Stew
10.0 years ago by
Stew1.4k
Cambridge
Stew1.4k wrote:

There are a number of peak callers available for chIP seq data. We are running MACS and SWEMBL and using overlaps but I would like some feedback about your experiences with chIP seq peak callers. I am aware of the ChIP-Seq Challenge but this was far from a complete study. What do you use?

chip-seq peak-calling • 13k views
ADD COMMENTlink modified 3.1 years ago by macmath140 • written 10.0 years ago by Stew1.4k
8
gravatar for Istvan Albert
10.0 years ago by
Istvan Albert ♦♦ 83k
University Park, USA
Istvan Albert ♦♦ 83k wrote:

Here is a paper that might be of interest:

A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments

We use our self developed method called GeneTrack (also discussed in the comparison above).

ADD COMMENTlink written 10.0 years ago by Istvan Albert ♦♦ 83k
4
gravatar for Madelaine Gogol
10.0 years ago by
Madelaine Gogol5.1k
Kansas City
Madelaine Gogol5.1k wrote:

I use MACS, it seems pretty good to me.

ADD COMMENTlink written 10.0 years ago by Madelaine Gogol5.1k
3
gravatar for Mikael Huss
10.0 years ago by
Mikael Huss4.7k
Stockholm
Mikael Huss4.7k wrote:

I typically use SISSRs or MACS for transcription factor ChIP-seq, and CCAT for histone mark ChIP-seq.

ADD COMMENTlink written 10.0 years ago by Mikael Huss4.7k
3
gravatar for Radhouane Aniba
8.6 years ago by
Radhouane Aniba760 wrote:

QuEST is a good tool to use for Chip-Seq data analysis, I found it very easy to use and it can handle at the same time TF Chip-Seq and Histone Mark Chip-seq It is however a good practice to use more than one tool and then overlap the results, the paper that Istvan pointed to is a good one because it present an overview of the different approaches used for peak estimation, not all the tools use the same algorithm so we always have to expect difference even not so big but it depends on how stringeant are you in calculating your peaks. QuEST also allow the cration of wig and bed files that you can postprocess or visualize at UCSC Genome Browser.

There is also an interesting paper by Pepke et al called "Computation of Chip-Seq and RNA-seq studies" that could be useful for you

Hope that helps

ADD COMMENTlink written 8.6 years ago by Radhouane Aniba760
3
gravatar for Ying W
8.6 years ago by
Ying W4.0k
South San Francisco, CA
Ying W4.0k wrote:

The encode project has looked at multiple chip-seq peak callers and found that the ones that are most reproducible are MACS and PeakSeq

see figure2 here: http://www.stat.washington.edu/qli/IDR101.pdf

ADD COMMENTlink written 8.6 years ago by Ying W4.0k
1
gravatar for Ming Tang
3.8 years ago by
Ming Tang2.6k
Houston/MD Anderson Cancer Center
Ming Tang2.6k wrote:

I collected some callers here https://github.com/crazyhottommy/ChIP-seq-analysis#peak-calling

ADD COMMENTlink written 3.8 years ago by Ming Tang2.6k
0
gravatar for Dan D
6.7 years ago by
Dan D7.0k
Tennessee
Dan D7.0k wrote:

A second vote for MACS 1.4.2. Aside from being open-source and well-documented, an interesting benefit is that the author tries to force you into the MACS user group in order to download the software. This seems annoying, but it's actually a huge help because Tao Liu quickly responds to user group queries and the discussions are very informative to follow.

ADD COMMENTlink written 6.7 years ago by Dan D7.0k
0
gravatar for dnaseiseq
6.3 years ago by
dnaseiseq200
United Kingdom
dnaseiseq200 wrote:

Here some peak callers are discussed

Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, et al. (2013) Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data. PLoS Comput Biol 9(11): e1003326. doi:10.1371/journal.pcbi.1003326

http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003326

ADD COMMENTlink written 6.3 years ago by dnaseiseq200
0
gravatar for boczniak767
3.8 years ago by
boczniak767680
Poland
boczniak767680 wrote:

I've used BayesPeak running in R. It is much easier to install than MACS (failed for me), which require some (strange to me) files.

But I'm not sure how it handle paired-end data and how to include biological replicates, so I can't recommend it. I'm still searching...

ADD COMMENTlink written 3.8 years ago by boczniak767680
0
gravatar for macmath
3.1 years ago by
macmath140
France
macmath140 wrote:

This is an interesting tool https://github.com/gersteinlab/MUSIC

ADD COMMENTlink written 3.1 years ago by macmath140
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