Question: How to select top significant ChiPseq peaks from MACS2 output file
1
gravatar for Mike
2.9 years ago by
Mike1.3k
UK
Mike1.3k wrote:

Hi all,

I have Macs2 output results in xls format , there are 10 columns in results files (including -log10(pvalue), fold_enrichment & -log10(qvalue), How to select top significant peaks from this file.

Thanks in advance

chip-seq peaks macs2 • 3.2k views
ADD COMMENTlink modified 2.9 years ago by dariober10k • written 2.9 years ago by Mike1.3k
2
gravatar for igor
2.9 years ago by
igor8.1k
United States
igor8.1k wrote:

Since p- and q- values are measures of significance, you can sort by those values. Since they are -log10, the most significant are the one with the highest values.

ADD COMMENTlink written 2.9 years ago by igor8.1k

Great, Thanks a lot,

And what about fold_enrichment ?

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by Mike1.3k
1
gravatar for dariober
2.9 years ago by
dariober10k
WCIP | Glasgow | UK
dariober10k wrote:

In practice I would suggest to look at some peaks with different fold changes to get a feel for what a sensible threshold should be for a peak to be convincing. Often I find that peaks with fold change ~2 don't look "peaky" at all so I discard anything below that threshold. Then for ranking peaks, it shouldn't matter very much if you use fold change, p-value or qvalue since these are very well correlated.

Also, take care that peaks with very high fold change (or very low p/q value) can be suspicious.

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by dariober10k

True. You can also use something like IDR to refine your peak list.

But it really depends on what your goal is. I've seen papers where they select the top 500,000 peaks. Clearly, at those numbers, many of them are not going to be very good at all.

ADD REPLYlink written 2.9 years ago by igor8.1k
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