Question: Which Chip Seq Peak Callers Do You Use?
11
gravatar for Stew
7.8 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 • 9.8k views
ADD COMMENTlink modified 11 months ago by macmath120 • written 7.8 years ago by Stew1.4k
8
gravatar for Istvan Albert
7.8 years ago by
Istvan Albert ♦♦ 75k
University Park, USA
Istvan Albert ♦♦ 75k 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 7.8 years ago by Istvan Albert ♦♦ 75k
4
gravatar for Madelaine Gogol
7.8 years ago by
Madelaine Gogol4.9k
Kansas City
Madelaine Gogol4.9k wrote:

I use MACS, it seems pretty good to me.

ADD COMMENTlink written 7.8 years ago by Madelaine Gogol4.9k
3
gravatar for Mikael Huss
7.8 years ago by
Mikael Huss4.6k
Stockholm
Mikael Huss4.6k wrote:

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

ADD COMMENTlink written 7.8 years ago by Mikael Huss4.6k
3
gravatar for Radhouane Aniba
6.4 years ago by
Radhouane Aniba750 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 6.4 years ago by Radhouane Aniba750
3
gravatar for Ying W
6.4 years ago by
Ying W3.7k
South San Francisco, CA
Ying W3.7k 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 6.4 years ago by Ying W3.7k
1
gravatar for Ming Tang
20 months ago by
Ming Tang2.2k
Houston/MD Anderson Cancer Center
Ming Tang2.2k wrote:

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

ADD COMMENTlink written 20 months ago by Ming Tang2.2k
0
gravatar for Dan D
4.6 years ago by
Dan D6.3k
Tennessee
Dan D6.3k 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 4.6 years ago by Dan D6.3k
0
gravatar for dnaseiseq
4.2 years ago by
dnaseiseq190
United Kingdom
dnaseiseq190 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 4.2 years ago by dnaseiseq190
0
gravatar for boczniak767
20 months ago by
boczniak767590
Poland
boczniak767590 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 20 months ago by boczniak767590
0
gravatar for macmath
11 months ago by
macmath120
France
macmath120 wrote:

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

ADD COMMENTlink written 11 months ago by macmath120
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