[BioC] 'SRAdb useful for visualizing BAM files'

[Jack Zhu]

> ---------- 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

   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
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>