On Sat, Apr 10, 2010 at 5:26 PM, Sean Davis <seandavi@gmail.com> wrote:

> Moved over to bioc-devel.
>
> On Sat, Apr 10, 2010 at 3:28 PM, Michael Lawrence
> <lawrence.michael@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.
>
>
Mostly out of curiosity, are you guys interfacing with IGV through the HTTP
interface or directly embedding it through rJava? My attempts at integrating
with Java-based browsers at the Java level have not met with much success,
which is unsurprising given that they are designed as GUI applications, not
libraries.


> Sean
>
> > On Sat, Apr 10, 2010 at 7:42 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>
> <
> 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
> >> >>
> >> >> _______________________________________________
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> >> >
> >>
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