Question: Peak calling with MACS for DNase-seq data and Peak annotation by Homer
gravatar for Bioinformatist Newbie
3.4 years ago by
Bioinformatist Newbie230 wrote:

I used macs 1.4 and macs 2 for peak calling. Then I used Homer for peak annotation to hg19. Peak scores ranges from 3205.08 to 50 and 342.34 to 2 respectively. The number of peaks identified are 65229 and 74979 respectively. I used the default parameters in both cases. Why is there so much variation in peak scores? what is the role of this peak score ? It is not clear from the Homer website. 

High peak score means that there are more chances of true positive peak? If yes, then what could be the right threshold to filter out the peaks?

In the supplementary material of a paper I found the information that they used Homer for chip-seq peaks identification and filter the peaks by peak score >10, but there they are not mentioning a reason behind this threshold.

peak calling dnase-seq homer macs • 2.0k views
ADD COMMENTlink modified 3.4 years ago by Ian5.4k • written 3.4 years ago by Bioinformatist Newbie230

I guess MACS is responsible for the difference, not HOMER.

ADD REPLYlink written 3.4 years ago by Zaag720
gravatar for Ian
3.4 years ago by
University of Manchester, UK
Ian5.4k wrote:

I hope I understood you correctly, but MACS1.4 transforms the Pvalue -10log10(P), where as MACS2 takes the -log10 of the Pvalue. This explains the 10 fold different you are seeing.

ADD COMMENTlink written 3.4 years ago by Ian5.4k

1- Difference in score is what you explained but how to interpret the difference in the number of peaks?

2- Some peaks have high score while others have low score. How this score is calculated and what does it mean? Is it that high scoring peaks are having more chances of being true positives while low scoring peaks have a higher chances of being false positive peaks..?

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by Bioinformatist Newbie230
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