Annotating peaks with genes

Question

[V]

Hello,

I have run a 10x genomics multiome experiment and have a list of open chromatin regions that are statistically significant (open) in a cell population of interest.

Using the csv containing the genomic coordinates of these regions (human), is there an online tool that I can use to annotate them with the closest downstream gene? I've tried using GREAT, but it really is not that great, and it mostly just enriches for whatever it detects rather than annotating with the closest downstream/upstream genes.

Any online sites any of you would have to suggest would be greatly appreciated. Thank you,

Answer 1

[jared.andrews07]

I highly recommend trying ArchR. It has the capacity to deal with multi-omic data and can do some nice co-accessibility analyses to help tie ATAC peaks to genes. Not an online site, but very useful, especially for any sort of motif analyses.

Just grabbing the closest genes to each peak can be done via bedtools closest with your peaks and annotations of interest.

[V]

Thank you for pointing me in the right direction, very helpful. Much appreciated!

[jared.andrews07]

The ChIPseeker R package will also assign peaks to genes (and provides some viz functions, etc) if you need other alternatives.