Hi everyone,
I have analyzed ATAC-seq data using the nf-core ATAC-seq pipeline, and I have obtained peak files from MACS2. My goal is to create a Circos plot to visualize global chromatin accessibility changes across different chromosomes between two sample groups (e.g., A549-WT vs A549-RES).
Despite exploring various tools, I haven't been able to figure out how to generate this plot. Could anyone provide a step-by-step guide or recommend an easy way to accomplish this?
Any help or pointers would be greatly appreciated!
Thank you!
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written
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biology_inform •
1 answer
If you want to plot global accessibility, maybe you would like to plot the ATAC "signal", instead of specific peaks. In a very general manner: one strategy you could do is to generate bedGraph files from your BAM alignment files (e.g. using deepTools) and then get that information into R (with packages such as plyranges or rtracklayer). This will get you your "signal" tracks into GenomicRanges format. Then, you could use the R package circlize, for which there is ample documentation, to plot circular visualizations of these tracks.
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I've been exploring different visualization tools like Circos and shinyCircos, and I've noticed that they require an input file similar to a BED file. However, I'm having trouble creating this file. I have two groups, each with two replicates, and the input file also requires an additional column called "value" (image below). I'm not sure how to generate this file correctly. Could you provide guidance or an example on how to structure this file?