On Sat, Apr 10, 2010 at 5:26 PM, Sean Davis wrote: > Moved over to bioc-devel. > > On Sat, Apr 10, 2010 at 3:28 PM, Michael Lawrence > 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 wrote: > > > >> > ---------- Forwarded message ---------- > >> > From: Aaron Mackey > >> > Date: Sat, Apr 10, 2010 at 7:49 AM > >> > Subject: Re: [BioC] 'SRAdb useful for visualizing BAM files' > >> > To: Sean Davis > >> > Cc: Paul Shannon , bioc > >> > > >> > > >> > > >> > 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 > wrote: > >> >> > >> >> On Fri, Apr 9, 2010 at 9:40 PM, Paul Shannon > >> >> 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 > >> > > >> > >> _______________________________________________ > >> 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]] > > > > _______________________________________________ > > 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]]