Plot Rna-Seq Coverage Along A Genome, Bioconductor

Question

[Jimbo]

Hi,

I have some BAM files I've read into R as a GRanges object using readBamGappedAlignments()

I have done the same in order to make an annotated genome, GRanges object using makeTranscriptDbFromUCSC(), followed by transcriptsBy().

I can use countOverlaps, I want to plot my reads in the bamfile against the genome, and visualise it, as well as zooming in on different genes something like:

DIFFERENT READS:
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                            ------
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GENE           :---------------------------->

But preferably with more detail :)

Is there a "canned" way to . I have heard of a way to do it using GenomeGraphs, but the examples are for array data.

Apologies if this isn't the best arena for proposing this question! I appreciate it is quite specific. Thanks for your time.

Cheers

Answer 1

[Sean Davis]

I'd suggest using the rtracklayer package to interact with the UCSC genome browser or use the IGV viewer from the Broad. To interact with the latter from R, have a look at the SRAdb package which allows one to load data, scroll, zoom, and make screen captures, all from the R command line.

[Martin Morgan]

ggbio in the 'devel' branch (due for release next week) might be good here.

[Sean Davis]

Fairness in answering, I am one of the authors of SRAdb.

[Jimbo]

Thanks, I am looking into it, I notice an example in the vignette I'm going to see if I can bend it to my needs :)

[brentp]

wow! rtracklayer looks pretty useful. I just read the vignette, but, to view local bed files in UCSC, it uploads them to a session? cool. and pretty powerful in combination with SRAdb.

[Jimbo]

Cheers Martin, this looks potentially really good. Waiting for official R 2.14 release...