Peak calling tools ChIP-seq

EvP · 10-19-2015, 03:51 AM

Dear all,

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

Thanks,
Eunice

sdriscoll · 12-10-2015, 07:29 AM

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.

cascoamarillo · 01-14-2016, 12:37 PM

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:
http://www.slideshare.net/lucacozzuto/macs-course

Any thought/inputs would be appreciated. Thanks

saupra · 08-11-2017, 11:28 PM

Hi,

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)

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10-19-2015, 03:51 AM	#1
EvP Junior Member Location: Amsterdam Join Date: Oct 2015 Posts: 1	Peak calling tools ChIP-seq Dear all, What are the most widely used peak calling tools for ChIP-seq data at the moment? Thanks, Eunice

12-10-2015, 07:29 AM	#2
sdriscoll 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 */

01-14-2016, 12:37 PM	#3
cascoamarillo 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: http://www.slideshare.net/lucacozzuto/macs-course Any thought/inputs would be appreciated. Thanks Last edited by cascoamarillo; 01-14-2016 at 01:38 PM.

08-11-2017, 11:28 PM	#4
saupra Junior Member Location: india Join Date: Dec 2016 Posts: 4	Hi, 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)