Right, I understand that IGV is capable of this -- what I'm not clear about
is whether the NCBI's SRA is capable of "serving" the BAM files in this
fashion, and if the R SRAdb package is capable of managing these forms of
connections, or must I still download all the BAMs (via SRAdb or otherwise).

-Aaron

On Sat, Apr 10, 2010 at 10:42 AM, Jack Zhu <zhujack@mail.nih.gov> wrote:

> > ---------- Forwarded message ----------
> > From: Aaron Mackey <ajmackey@gmail.com>
> > Date: Sat, Apr 10, 2010 at 7:49 AM
> > Subject: Re: [BioC] 'SRAdb useful for visualizing BAM files'
> > To: Sean Davis <seandavi@gmail.com>
> > Cc: Paul Shannon <pshannon@systemsbiology.org>, bioc
> > <bioconductor@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@gmail.com> wrote:
> >>
> >> On Fri, Apr 9, 2010 at 9:40 PM, Paul Shannon
> >> <pshannon@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
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@stat.math.ethz.ch
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
>

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