Methods to integrate ATAC-seq and RNA-seq

Question

[Chris]

Hi all,

I found many papers doing this integration, so I am not sure which one is the best practice. Would you suggest your favorite paper or a tutorial to do this? Especially the tools to perform the integration. There is a paper I found that use deeptools R package but I only find a python package with the same name. I appreciate it! Seem ArchR or Signac can do this integration with single cell only but not bulk ATAC-seq.

[rizoic]

You can take a look at BETA which can help you enlist genes which are up/down regulated and have ATACseq signal within a certain distance from them.

Answer 1

[MolGeek]

One method is to annotate the peak list / differential accessibility list of the ATAC Seq with ChipSeeker using the nearest method to assign the peaks to genes. Then, you can integrade the ATACs using those genes, to the genes that are expressed in RNA Seq.

See methods in here for a more detailed explanation:

Integration of ATAC-Seq and RNA-Seq

[Chris]

Thank you. I also read this paper before and not sure the detail about using Pearson correlation in the integrate section of the paper. Would you suggest how to do next? Could not find a Github page of this paper. I used ChIPpeakanno instead of ChIPSeeker. I found this function of deeptools do Pearson correlation but not sure how it relate to RNA-seq data with up and down regulated genes:
https://deeptools.readthedocs.io/en/develop/content/tools/plotCorrelation.html

Answer 2

[Tao Zhu]

cisDynet has a good approach for integrating multiple samples for ATAC-seq and RNA-seq.