Overlapping cut and tag H3k27 peaks and ATAC-Seq peaks

Question

[new]

Hello

First post & new to this. I have peaks from cut & tag for H3K27ac (SEACR) and also for ATAC-Seq (MACS2)

I'd like to overlap them to get a file of overlapping peaks.

What is the best way to do this?

Thank you

[ATpoint]

In R one would use findOverlaps() or subsetByOverlaps() from the GenomicRanges package.

Answer 1

[Pierre Lindenbaum]

bedtools intersect is the answer. https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html

[new]

Ok. Thanks. Would you increase the size of the peaks first using bedtools slops?

[Trivas]

I would follow a standard ATAC-seq/ChIP-seq pipeline and include that within the MACS2 peak calling as discussed here:

ATAC-seq peak calling with MACS

[new]

Yes, I have done that. And used SEACR for the Cut & Tag peaks. Called narrow peaks for ATAC-Seq. Intersect with bedtools is not an issue, but don't know if there is anything I am not thinking of re broad peaks vs narrow peaks. Thanks anyway.

[rfran010]

One consideration is the amount of overlap you're looking for. Default behavior will take any amount of overlap. You can change this to require a greater amount or to allow a gap between the peaks.

I prefer a stricter threshold for overlapping peaks, where in this case you might require at least 25-50% of the ATAC peak is overlapped.

Also with bedtools pay attention to what you are outputting. In general, if you provide the ATAC-peaks as -a and K27ac as -b then the output will be the original ATAC-peaks that are marked by K27ac. I imagine this is your desired output, but if you wanted to see K27ac peaks that contained accessible regions, then you would input the K27ac peaks as -a.

Also, the default behavior is to output a line from -a for every overlap found in -b. Sometimes this isn't really an issue, but for example if you had a really large ATAC peaks covered by two separate K27ac peaks (assuming ATAC peaks are input as -a), then you would get the same ATAC-seq peak twice in the output file. I usually use the -u flag to keep a one line per peak ratio.

This is all obvious in their documentation which is comprehensive, and sorry if it's all obvious to you, but it wasn't obvious to me originally.

[new]

Thank you - it wasn't obvious to me, and is very helpful. Thanks!