Question: Coverage plot of a complete genome
0
gravatar for frymor2
8 weeks ago by
frymor210
frymor210 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
ADD COMMENTlink modified 8 weeks ago by hcinneyjuriya0 • written 8 weeks ago by frymor210

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 REPLYlink modified 8 weeks ago by h.mon32k • written 8 weeks ago by German.M.Demidov1.9k

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 REPLYlink written 8 weeks ago by scheitelt10

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

ADD REPLYlink written 8 weeks ago by German.M.Demidov1.9k
2
gravatar for Pierre Lindenbaum
8 weeks ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum133k wrote:

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

enter image description here

ADD COMMENTlink written 8 weeks ago by Pierre Lindenbaum133k

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

ADD REPLYlink written 8 weeks ago by frymor210

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 REPLYlink written 8 weeks ago by Pierre Lindenbaum133k

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 REPLYlink written 8 weeks ago by frymor210
1

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

ADD REPLYlink written 8 weeks ago by Pierre Lindenbaum133k

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

ADD REPLYlink written 8 weeks ago by frymor210
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