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?

-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

	[[alternative HTML version deleted]]

