Question: Single gene circos plot possible?
1
gravatar for frank_de_kievit
4.2 years ago by
United Kingdom
frank_de_kievit10 wrote:

Hi All,

I've sequenced the exons of tp53, and now I want to visualise my depth of sequencing. How would I do this best, given the area to show my figure on is rather small (+- 5cm * 8cm). My solution would be to make a small circos plot with a custom track, starting at exon1, to exon 11, skipping introns, and have only 1 track, which shows the depth of sequencing on the exon location.

I've not seen anyone do this before. Is it doable?

circos gene • 1.4k views
ADD COMMENTlink modified 4.1 years ago by Biostar ♦♦ 20 • written 4.2 years ago by frank_de_kievit10

Do you really want to use Circos, which is not known for being the simplest tool to use, for plotting such a simple thing? I would think it'd be easier to just use samtools depth with a bed file containing the exons and then load the output into R and simply plot that. Even using ggplot2 is likely going to prove simpler than Circos and I wonder if Circos' added capabilities are really needed for what you want.

ADD REPLYlink written 4.2 years ago by Devon Ryan91k

I'm looking for a tool, which is visually appealing, which shows the depth of sequencing across this single gene.

Could you supply any mockups of what you are suggesting ?

ADD REPLYlink written 4.2 years ago by frank_de_kievit10

Depending on how visually appealing you really need things to be, a screenshot of the coverage track and the annotation track from IGV might even suffice. Anyway, regarding my last comment just look up ggplot2, there are plenty of example images out there.

ADD REPLYlink written 4.2 years ago by Devon Ryan91k

That wouldn't work, since we are sequencing batches in the range of >100k ;) The plots are part of a generated pdf report for each sample (and at the moment we are brainstorming on how to visualise p53 coverage, so that's why I threw it out here).

ADD REPLYlink written 4.2 years ago by frank_de_kievit10

I would think something like you can see at Let’s Plot 3: Base pair resolution NGS (exome) coverage plots - Part 1 is what Devon or Frank was suggesting?

ADD REPLYlink modified 17 months ago • written 17 months ago by Wayne330

Yes, it can be done. You just add whole gene as a custom reference genome.

ADD REPLYlink written 4.2 years ago by Biomonika (Noolean)3.1k
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