Coverage plot of a complete genome

Question: Coverage plot of a complete genome

8 weeks ago by

frymor2 • 10 wrote:

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

coverage Plot

plot cnv coverage • 234 views

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modified 8 weeks ago by hcinneyjuriya • 0 • written 8 weeks ago by frymor2 • 10

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)

ADD REPLY • link modified 8 weeks ago by h.mon ♦ 32k • written 8 weeks ago by German.M.Demidov • 1.9k

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?

ADD REPLY • link written 8 weeks ago by scheitelt • 10

You can calculate the coverage per some window, smooth it with rolling median and plot in R - this is what I would do

ADD REPLY • link written 8 weeks ago by German.M.Demidov • 1.9k

8 weeks ago by

Pierre Lindenbaum ♦ 133k

France/Nantes/Institut du Thorax - INSERM UMR1087

Pierre Lindenbaum ♦ 133k wrote:

I wrote http://lindenb.github.io/jvarkit/WGSCoveragePlotter.html

enter image description here

ADD COMMENT • link written 8 weeks ago by Pierre Lindenbaum ♦ 133k

Thanks Pierre, this looks good. Is it possible to use a bam file with multiple read groups as an input here?

ADD REPLY • link written 8 weeks ago by frymor2 • 10

you meant that there is only more that one sample ? everything would be merged here, but I can add an option to only select a defined sample.

ADD REPLY • link written 8 weeks ago by Pierre Lindenbaum ♦ 133k

What I meant is, if there is a possibility to take a bam file with multiple samples, defined by separate read groups and use it as an input. I have a concatenated bam files I have merged from several single samples, for several reasons. Now I would like to plot this bam file, but to get the coverage separated by the single samples (e.g marked by the read groups). This should be something like the the facet_wrap in the R command ggplot. One row should represent one read group instead of a whole bam file.

Would this be possible?

ADD REPLY • link written 8 weeks ago by frymor2 • 10

I've just added an option --samples http://lindenb.github.io/jvarkit/WGSCoveragePlotter.html

ADD REPLY • link written 8 weeks ago by Pierre Lindenbaum ♦ 133k

thanks, I'll give it a go as soon as as possible and come back to you

ADD REPLY • link written 8 weeks ago by frymor2 • 10

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