Hi Aaron, Maybe there is need for serving BAM files for NCBI SRA runs somewhere. It seems that that will take a consortium to do it in terms of work and standards. I guess large consumers of public Next-Gen Sequencing data should lead this. Jack On Mon, Apr 12, 2010 at 9:32 AM, Aaron Mackey <ajmackey at="" gmail.com=""> wrote: > Thanks for the clarification.? I was confused by someone's earlier statement > about SRAdb having an interface to IGV, and jumped to the conclusion that > SRA was now supplying BAM files, not just fastq -- my mistake. > > -Aaron > > On Sun, Apr 11, 2010 at 1:04 PM, Sean Davis <seandavi at="" gmail.com=""> wrote: >> >> On Sun, Apr 11, 2010 at 12:41 PM, Aaron Mackey <ajmackey at="" gmail.com=""> wrote: >> > Right, I understand that IGV is capable of this -- what I'm not clear >> > about >> > is whether the NCBI's SRA is capable of "serving" the BAM files in this >> > fashion, and if the R SRAdb package is capable of managing these forms >> > of >> > connections, or must I still download all the BAMs (via SRAdb or >> > otherwise). >> > >> >> Hi, Aaron. ?NCBI SRA does not serve BAM files at all, only fastq >> files. ?The functionality of interfacing with IGV is not directly >> related to the SRA querying facilities, really. ?SRAdb IGV interfacing >> is through filenames or URLs; no connections are really managed in R >> to make this happen. ?Only filenames or URLs are passed via an http >> protocol from R to IGV. ?The rest is done by IGV. ?Since IGV is quite >> capable of reading from a URL in a random-access fashion, BAM files on >> an appropriate server can be read without downloading. >> >> Hope that helps, >> Sean >> >> > On Sat, Apr 10, 2010 at 10:42 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=anony mous&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/r epos',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 >> >> > >> > >> > > >