Coverage plots

[pouriamomayyezi]

Hello Guys,

I've just started analysing my first sc ATAC seq dataset using SnapAtac2 and I find it very user friendly and effective. Thank you for a great set of tools.
I've been able to preprocess, batchcorrect and cluster without any major problems.

I'm however having problems creating coverage plots that look good. I've tried using seaborn with and mathplotlib but nothing that I create myself looks nearly as good as anything found in published papers.

Is there a built in function for doing this in SnapAtac2 that I'm missing? Or can you recommend a library in python that would have this as a built in function?
I would like to create a plot similar to this for the region of my interest:

https://training.galaxyproject.org/training-material/topics/epigenetics/images/atac-seq/atac-seq.jpeg

Very thankful for any sort of advice I could get regarding this.

All the best
Pouria

[ejarmand]

Hi Pouria, most coverage plots in papers will be made using a genome browser. To generate them you would export your tracks (usually as a bigwig; run snap.ex.export_bigwig), and upload them to the browser.

You can see many examples of IGV browsers on catlas, and IGV is easy to install locally https://igv.org/.

Other popular browsers for epigenome data are:

• the washu epigenome browser https://epigenomegateway.wustl.edu/,
• jbrowse https://jbrowse.org/jb2/
• the ucsc genome browser https://genome.ucsc.edu/

Off the top of my head I wouldn't know how to create the very bottom track with multiple histone marks, but this should help with other visualization.

[pouriamomayyezi]

Thank you very much for the help!

[kaizhang]

Please also see #108