Gene body coverage plot
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svenbioinf • 0
@svenbioinf-11239
Last seen 3 months ago
Münster

Dear bioconductor community,

is there an R tool that generates a coverage plot around gene bodies like the one created by the RSeQC tool? Preferably working on region information stored in GenomicRanges objects. I just found a similar question here link which is 6 years ago.

Some input on this is appreciated! Thank you!

coveragePlot

plot gene GenomicRanges Coverage R • 433 views
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Guido Hooiveld ★ 3.3k
@guido-hooiveld-2020
Last seen 2 days ago
Wageningen University, Wageningen, the …

I always use a pipeline in which functions of the RSeQC tool are called (incl. the gene coverage plot).

Having said this, in the past I came across an R package called genecovr (link) that based on the available info might do what you are looking for ("The genecovr package provides functionality for evaluating gene body coverage and other metrics in genome assemblies. The central measurement unit is a gene or transcript model"). Also see the vignette.

Also, I know that the R package accompanying the QoRTs tool is used to make visualizations of QC metrics, including gene coverage plots. Again, I don't have any hands-on experience with it, so I cannot comment on its compatibility with your output files...

<<forgot to add>> When browsing Bioconductor packages I also noticed the package CoverageView. Although primarily designed for the visualization of ChIp-seq-like experiments, "additionally, CoverageView can also be used in RNA-seq experiments in order to compare how the coverage is distributed along the transcriptome."

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@kentriemondy-14219
Last seen 1 day ago
Denver, University of Colorado Anschutz…

The calculateCoverageProfileList function from the RCAS package can generate summary coverage values across genomic features (5' UTR, cds, 3' UTR, introns, etc.) in an RNA aware manner.

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