I’ve been searching for a way to plot bigwig coverage from my ATAC-seq data and illustrate differences in open chromatin at particular loci. I want to avoid having to screenshot tracks in IGV browser because its tedious and laborious.
I have recently come across the wiggleplotr package, which I really like but some more tweaks to this tool would make it even more widely usable tool, especially for programming noobs like myself.
The documentation is clear and I managed to generate all the necessary metatables to get it to work in my genome of choice. However, the package is very much geared towards RNA-seq data and in particular plotting coverage over alternative splice forms of a single gene.
I would like a broader solution for plotting bigwig coverage at a genetic locus as I am not interested in alternative splice forms per se. I would like a way to centre the plot at a certain gene but also include any flanking genes in the plot for accuracy - wiggleplotr only seems to deal with one gene at a time.
Has anyone managed to use wiggleplotr for other NGS datasets or can someone recommend a viable alternative?
Dr Michael Borg
Gregor Mendel Institute
Dr. Bohr Gasse 3