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

[Jack Zhu]

Hi Michael,

Thanks for your interest and suggestions.

On Sun, Apr 11, 2010 at 12:08 AM, Michael Lawrence
<lawrence.michael at gene.com> wrote:
>
>
> On Sat, Apr 10, 2010 at 5:26 PM, Sean Davis <seandavi at gmail.com> wrote:
>>
>> 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.
>>
>
> Mostly out of curiosity, are you guys interfacing with IGV through the HTTP
> interface or directly embedding it through rJava?

We are using  the HTTP interface, specifically using IGV listening
port to transfer file paths and parameters to IGV.  Although I am not
familiar with rJava, our method apparently has more limitations than
rJava API.

Example in SRAdb:

   oad2IGV_url <-
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
   browseURL(load2IGV_url)

> 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.

I guess GUI based Java applications are hard to be integrated.

Jack

>
>>
>> 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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