Question: Extracting read coverage data from a Gviz AlignmentsTrack
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gravatar for willbradshaw
3 months ago by
willbradshaw0 wrote:

I'm using Gviz to make read-coverage and Sashimi plots for a paper, and I'd like to extract information about how many reads contribute to each splice junction in the Sashimi plot. These numbers must be inferred at some point since Gviz is generating the AlignmentsTrack object directly from the BAM file, but it's not clear to me whether it's possible for a user to get access to the intermediate steps used to generate the Sashimi plot. Is there a way to do this?

gviz sashimi • 75 views
ADD COMMENTlink modified 12 weeks ago by Robert Ivanek660 • written 3 months ago by willbradshaw0
Answer: Extracting read coverage data from a Gviz AlignmentsTrack
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gravatar for Robert Ivanek
12 weeks ago by
Robert Ivanek660
Switzerland
Robert Ivanek660 wrote:

Hi, You can simply read in the part of your BAM file with GAlignments function and afterwards extract junction counts with summarizeJunctions, both function come from GenomicAlignments package.

ADD COMMENTlink written 12 weeks ago by Robert Ivanek660
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