Question: Plot Rna-Seq Coverage Along A Genome, Bioconductor
5
gravatar for Jimbo
7.1 years ago by
Jimbo120
Jimbo120 wrote:

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:
                 ------
                       ------
                            ------
                   ------
                               ------

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

genome R bioconductor rna • 3.2k views
ADD COMMENTlink modified 3.5 years ago by Biostar ♦♦ 20 • written 7.1 years ago by Jimbo120
5
gravatar for Sean Davis
7.1 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

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.

ADD COMMENTlink written 7.1 years ago by Sean Davis25k
1

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

ADD REPLYlink written 7.1 years ago by Martin Morgan1.6k

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

ADD REPLYlink written 7.1 years ago by Sean Davis25k

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 :)

ADD REPLYlink written 7.1 years ago by Jimbo120

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.

ADD REPLYlink written 7.1 years ago by brentp22k

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

ADD REPLYlink written 7.1 years ago by Jimbo120
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