[Bioc-devel] [BioC] 'SRAdb useful for visualizing BAM files'

[Sean Davis]

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.

Sean

> 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
>> problem.
>>
>> Example using an URL directly:
>>
>>
>> http://www.broadinstitute.org/igv/dynsession/igv.jnlp?user=anonymous&sessionURL=http://watson.nci.nih.gov/~zhujack/SRAdb_bam/SRR036007.chr1.hg18.bwa.sorted.bam&locus=chr1:1-1000000<http://www.broadinstitute.org/igv/dynsession/igv.jnlp?user=anonymous&sessionURL=http://watson.nci.nih.gov/%7Ezhujack/SRAdb_bam/SRR036007.chr1.hg18.bwa.sorted.bam&locus=chr1:1-1000000>
>>
>>   This will launch a new IGV and access the bam from an URL.
>>
>> Example using the SRAdb package:
>>
>>        library(SRAdb)
>>        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.
>>
>> Jack
>>
>>
>>
>>
>> >
>> > -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
>> ',type='source')
>> >>
>> >> There is a vignette included.
>> >>
>> >> Sean
>> >>
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>> >
>>
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