Visualise ChIP-seq data over a full genome/chromosome with genes and transposons

Question

[alebaars_98]

Hello everyone,

My project is coming to a close, and I'm visualizing my data and have started writing. There is a type of graph I want to make, but unfortunately, I cannot for the life of me figure out what software to use best.

Specifically, I want to visualize the coverage of my chromatin marks over the full genome (or a single chromosome to use as an example) with the genes and transposons highlighted, like with figure 1A and 2A of this article. I already have the chromatin visualized around the TSS with deeptools, but I cannot find a way to do it at a larger scale. An important thing to note is that I cannot use BAM files, only bigwig (or converted to bedgraph, that's also fine), because my bigwigs are normalized for MNase. Also, it needs to be able to work with a custom genome (not from e.g. NCBI).

Does anyone recognize the programme(s) used in the mentioned figure, or know another way to get the figure I want? Other tips and tricks are also welcome. Thanks in advance.

Answer 1

[ATpoint]

I like trackplot: Fast and minimal dependency standalone R script to generate IGV style locus tracks from bigWig files

Then there is of course gviz https://bioconductor.org/packages/devel/bioc/vignettes/Gviz/inst/doc/Gviz.html

Basically, if you have the coverage (e.g. bigwig) files loaded into R you can also just do some ggplot magic and then arrange the individual plots as you like.

[alebaars_98]

Trackplot seems very similar in style to the figures described and looks promising. Thank you!