Plotting ATAC-seq data over RNA-seq?

Question

[alphaflylizard]

Hi everyone,

I am new to this space and have no bioinformatics background -- with very limited knowledge on data processing. So I apologize ahead of time if any of my questions are extremely stupid or make no sense :)

I did manage to process my ATAC-seq data using the nfcore/atacseq bioinformatics analysis pipeline. I then proceeded with HOMER commands to do the Differential analysis between my two conditions (genotype A vs genotype B). From there I manually separated my called peak files with an FDR cut off 0.05 into peaks going UP or DOWN based on the log fold change. All of these files are .txt files.

I would now like to plot this ATAC-seq peaks across an RNA-seq FPKM data (.txt file) set that I have from more genotypes, including those I did the binary ATAC-seq comparison for.

What is the correct way to do this? What is the correct set of commands to use? Is the HOMER command mergePeaks the right way to go about this?

How do I visually represent the changes I see?

Thank you so much for the help!

Answer 1

[rfran010]

I think you could annotate your atac peaks with gene data. http://homer.ucsd.edu/homer/ngs/annotation.html

You can then plot RNA-seq data from up or down peaks. When doing this, you may also further distinguish Promoter Peaks vs Intergenic Peaks, etc... Although, you may have more success with gene ontology of open vs closed peaks, since in my experience ATAC-seq changes do not always strongly correlate with RNA-seq changes of nearby genes, even when it is a promoter ATAC-seq peak.

In addition to plots, you can generate bigwig (binary version of a bedgraph) files to visualize the signal over genomic loci. Then you could find an ATAC-seq peak of interest that maybe has RNA-seq signal of interest...