How to get a list of gene names from macs2 peaks

Question

[Daniel]

Hello,

I have a fairly straightforward question that is surprisingly difficult to answer (or find relevant content) online. I have used macs2 to call peaks for two samples. I have multiple output files, being .narrowPeak, .xls, and .bed files. How do I use these to get a list of gene names that are associated with the peaks? My end goal is to see which peaks occur in one group vs another.

I'd think the .bed file has this, but there is no chromosome info associated with the coordinates.

Answer 1

[jared.andrews07]

Use ChIPseeker or HOMER to annotate them based on your annotations of interest.

MACS2 does not annotate peaks.

[Daniel]

I see, thank you. Based on my understanding, macs2 is one of the more commonly used tools for chip-seq. If it does not annotate peaks, how do most users use its output, especially in publications? Is it mostly used for visual validation that a peak exists for a gene of interest (for example in IGV)?

Thanks!

[jared.andrews07]

MACS is a peak caller. That's it. People use it to get regions of enriched signal over background. What they do after that varies wildly.

In some cases, people identify unique peaks or compare signal at peaks between groups of samples (e.g. with DiffBind or csaw). In other cases, they may do motif analyses for the peak regions to identify co-occupying TFs/TF families (e.g. with HOMER or the MEME suite).

Some studies just use the peaks for identifying genes a given TF may regulate and tie it back to meaningful gene expression analyses (TF knockdown/out/perturbation). Or they may use it in a purely descriptive manner alongside other data.

In short, it just depends, and you should spend some time thinking carefully about the questions you hope to answer with your data. Read some papers, see what others have done, and plan out what you should do.

[Daniel]

Ahh, I see. Thank you very much.