In a paper I was reading i have found the attached image. It shows the duplication of specific chromosomes in different yeast strains after treatment with antibiotics.
I was wondering how can one plot the whole genome in such a way? Are there any tools or R packages to get such a result?
thanks
tbh, it looks like a CNV caller worked here =) the plots looks too uniform - which means they were likely GC/library size normalized before plotting
or it is a rolling median across the coverage precalculated in some windows (e.g. 50kbps)
yes, This is true, but it doesn't really answer the question. The question was how this plot was done. can some please help me too?
You can calculate the coverage per some window, smooth it with rolling median and plot in R - this is what I would do