Entering edit mode
9.5 years ago
frank_de_kievit
▴
10
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?
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 depthwith 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.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 ?
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.
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).
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?
Yes, it can be done. You just add whole gene as a custom reference genome.