plot genome using RCircos

Question

[hbdhondge]

I want to paint some specific genes from H37rv genome assembly. Can anyone suggest me appropriate way to do it, as this assembly is not there in UCSC ?

[cpad0112]

Do you have cytoband information for this genome?

Answer 1

[bernatgel]

You can use karyoploteR for that. It will draw the genome as lines instead of a circle, but it can work with any genome as long as you give it the chromosome names and lengths. It is not restricted to any species or any data provider such as UCSC or Ensembl.

There's a small tutorial on how to draw genes in the genome that uses the GRCh38 human genome and a tutorial on how to plot a custom genome. If you combine these two you can create the plots you need.

And you can also take a look at this biostars question with some code on plotting data on a customa genome (yeast in this case).