[Bioc-devel] [BioC] 'SRAdb useful for visualizing BAM files'
seandavi at gmail.com
Sun Apr 11 02:26:54 CEST 2010
Moved over to bioc-devel.
On Sat, Apr 10, 2010 at 3:28 PM, Michael Lawrence
<lawrence.michael at gene.com> wrote:
> Just thought I would point out that the rtracklayer package was designed as
> a common, abstract interface for genome browsing. Right now, UCSC is the
> only supported backend, but it has been tested with alternative backends. It
> would be ideal, in my opinion, if this IGV - R integration would fit into
> the rtracklayer API. We're looking at integrating IGB with rtracklayer, so
> it would be nice if everything was behind a common interface.
Thanks, Michael, for the suggestion. This sounds like a good idea.
Jack and I will look into how the very limited API that IGV offers
might fit into the rtracklayer interface.
> On Sat, Apr 10, 2010 at 7:42 AM, Jack Zhu <zhujack at mail.nih.gov> wrote:
>> > ---------- Forwarded message ----------
>> > From: Aaron Mackey <ajmackey at gmail.com>
>> > Date: Sat, Apr 10, 2010 at 7:49 AM
>> > Subject: Re: [BioC] 'SRAdb useful for visualizing BAM files'
>> > To: Sean Davis <seandavi at gmail.com>
>> > Cc: Paul Shannon <pshannon at systemsbiology.org>, bioc
>> > <bioconductor at stat.math.ethz.ch>
>> > Thanks for the info Sean. Will this use the remote-BAM access
>> > capabilities of IGV, or does it entail downloading the entire BAM from
>> > SRA before viewing?
>> Yes, IGV has capabilities of using http random access, which means
>> data is dynamically loaded into IGV viewing window without loading an
>> entire BAM file in advance. Please see details here:
>> http://www.broadinstitute.org/igv/ControlIGV . From our experience,
>> the random data access (Google Map like) in IGV make data loading
>> faster and loading large multiple tracks possible without huge memory
>> Example using an URL directly:
>> This will launch a new IGV and access the bam from an URL.
>> Example using the SRAdb package:
>> sra_dbname <- 'SRAmetadb.sqlite'
>> sra_con <- dbConnect(dbDriver("SQLite"), sra_dbname)
>> ## If there is no IGV running in your computer, the following
>> statement will launch a new IGV and load BAM files to it:
>> files = list.files(system.file('extdata', package = "SRAdb"),
>> pattern='.bam$', full.names=TRUE)
>> load2newIGV(files, locus='chr1:1-1000000')
>> Please let me know if you have any questions.
>> > -Aaron
>> > On Fri, Apr 9, 2010 at 10:21 PM, Sean Davis <seandavi at gmail.com> wrote:
>> >> On Fri, Apr 9, 2010 at 9:40 PM, Paul Shannon
>> >> <pshannon at systemsbiology.org> wrote:
>> >> > Martin suggests ("An Introduction to Rsamtools", April 8th, 2010):
>> >> >
>> >> > 'Users might also find the interface to the integrative genome
>> browser (IGV) in SRAdb useful for visualizing BAM files.'
>> >> >
>> >> > I have tried googling many versions of the relevant words, and cannot
>> find anything about this. Is it an R interface to IGV? Any ideas about how
>> I can find out more?
>> >> >
>> >> > Thanks!
>> >> Hi, Paul.
>> >> SRAdb is an R package for searching the NCBI SRA database in a more
>> >> user-friendly way and for accessing the data in SRA. One of the
>> >> facilities that is included is an interface to start IGV and load BAM
>> >> files of interest directly from R. The package has been submitted to
>> >> bioconductor and is in review. However, if you like, you can
>> >> potentially install it now (assuming that you can deal with source
>> >> package installation) by doing:
>> >> install.packages('SRAdb',repos='http://watson.nci.nih.gov/R/repos
>> >> There is a vignette included.
>> >> Sean
>> >> _______________________________________________
>> >> Bioconductor mailing list
>> >> Bioconductor at stat.math.ethz.ch
>> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> >> Search the archives:
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> Search the archives:
> [[alternative HTML version deleted]]
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
More information about the Bioc-devel