Go Back   SEQanswers > Applications Forums > Epigenetics

Similar Threads
Thread Thread Starter Forum Replies Last Post
ChIP-Seq Peak Calling tools oxydeepu Bioinformatics 3 01-18-2013 01:42 AM
ChIP-seq peak calling from replicates ttnguyen Bioinformatics 4 08-10-2011 02:21 AM
ChIP-Seq: Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing bench Newsbot! Literature Watch 0 11-10-2010 03:40 AM

Thread Tools
Old 10-19-2015, 03:51 AM   #1
Junior Member
Location: Amsterdam

Join Date: Oct 2015
Posts: 1
Default Peak calling tools ChIP-seq

Dear all,

What are the most widely used peak calling tools for ChIP-seq data at the moment?

EvP is offline   Reply With Quote
Old 12-10-2015, 07:29 AM   #2
I like code
Location: San Diego, CA, USA

Join Date: Sep 2009
Posts: 438

MACS or Homer. Homer has a few peak calling modes that control the type and size of peaks it finds. MACS is more of a straight ahead peak caller that just looks for peaks of any width. at least that's how I think of the two.
/* Shawn Driscoll, Gene Expression Laboratory, Pfaff
Salk Institute for Biological Studies, La Jolla, CA, USA */
sdriscoll is offline   Reply With Quote
Old 01-14-2016, 12:37 PM   #3
Senior Member
Location: MA

Join Date: Oct 2010
Posts: 160

Hi all,
And what about MeDIP-seq (not ChIP-seq)? I guess the answer would be the same, but what parameters keep/change?
I'm working on a Illumina IP library (50 bp SE) made after inmunoprecipitate genomic DNA fragments with antibodies which detect methylated bases. I've seen one paper using MACS with these kind of data, thought no specify any parameters used. Right now, I don't have control/input.
Eg. after using MACS, it says no paired peaks were found so I should go with the --nomodel option, but I'm guessing about --shiftsize since there is no TF I'm looking for (just nucleotide methylation); would it be important that --shiftsize number?
One more thing I'd like to ask is, not having control/input I've heard I should use the --nolambda option. Actually that's from this ppt tutorial:

Any thought/inputs would be appreciated. Thanks

Last edited by cascoamarillo; 01-14-2016 at 01:38 PM.
cascoamarillo is offline   Reply With Quote
Old 08-11-2017, 11:28 PM   #4
Junior Member
Location: india

Join Date: Dec 2016
Posts: 4


I am trying to analyze data for factor which does not behave typically as transcription factor. I used macs and homer for peak calling. macs2 is giving me hardly 20-30 peaks while Homer is giving about 20000 peaks. macs2 is not picking up peaks which i can easily visualize in IGV. How can i be sure which peak caller to use and how can I filter peaks from Homer data (based on what criteria)
saupra is offline   Reply With Quote

chip seq, chip-seq, peak calling

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 02:44 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO