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Question: 'SRAdb useful for visualizing BAM files'
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gravatar for Paul Shannon
7.6 years ago by
Paul Shannon1.1k
Paul Shannon1.1k 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! - Paul
ADD COMMENTlink modified 7.6 years ago by Jack Zhu170 • written 7.6 years ago by Paul Shannon1.1k
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gravatar for Sean Davis
7.6 years ago by
Sean Davis21k
United States
Sean Davis21k 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',typ e='source') There is a vignette included. Sean
ADD COMMENTlink written 7.6 years ago by Sean Davis21k
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]]
ADD REPLYlink written 7.6 years ago by Aaron Mackey200
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gravatar for Jack Zhu
7.6 years ago by
Jack Zhu170
Jack Zhu170 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=anonymou s&sessionURL=http://watson.nci.nih.gov/~zhujack/SRAdb_bam/SRR036007.ch r1.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 >
ADD COMMENTlink written 7.6 years ago by Jack Zhu170
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. Michael On Sat, Apr 10, 2010 at 7:42 AM, Jack Zhu <zhujack@mail.nih.gov> wrote: > > ---------- Forwarded message ---------- > > From: Aaron Mackey <ajmackey@gmail.com> > > Date: Sat, Apr 10, 2010 at 7:49 AM > > Subject: Re: [BioC] 'SRAdb useful for visualizing BAM files' > > To: Sean Davis <seandavi@gmail.com> > > Cc: Paul Shannon <pshannon@systemsbiology.org>, bioc > > <bioconductor@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.chr 1.hg18.bwa.sorted.bam&locus=chr1:1-1000000<http: www.broadinstitute.o="" rg="" igv="" dynsession="" igv.jnlp?user="anonymous&amp;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@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 > > > > _______________________________________________ > 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]]
ADD REPLYlink written 7.6 years ago by Michael Lawrence9.8k
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). -Aaron On Sat, Apr 10, 2010 at 10:42 AM, Jack Zhu <zhujack@mail.nih.gov> wrote: > > ---------- Forwarded message ---------- > > From: Aaron Mackey <ajmackey@gmail.com> > > Date: Sat, Apr 10, 2010 at 7:49 AM > > Subject: Re: [BioC] 'SRAdb useful for visualizing BAM files' > > To: Sean Davis <seandavi@gmail.com> > > Cc: Paul Shannon <pshannon@systemsbiology.org>, bioc > > <bioconductor@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.chr 1.hg18.bwa.sorted.bam&locus=chr1:1-1000000<http: www.broadinstitute.o="" rg="" igv="" dynsession="" igv.jnlp?user="anonymous&amp;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@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]]
ADD REPLYlink written 7.6 years ago by Aaron Mackey200
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=anonymou s&sessionURL=http://watson.nci.nih.gov/~zhujack/SRAdb_bam/SRR036007.ch r1.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/repo s',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 >> > > >
ADD REPLYlink written 7.6 years ago by Sean Davis21k
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@gmail.com> wrote: > On Sun, Apr 11, 2010 at 12:41 PM, Aaron Mackey <ajmackey@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@mail.nih.gov> wrote: > >> > >> > ---------- Forwarded message ---------- > >> > From: Aaron Mackey <ajmackey@gmail.com> > >> > Date: Sat, Apr 10, 2010 at 7:49 AM > >> > Subject: Re: [BioC] 'SRAdb useful for visualizing BAM files' > >> > To: Sean Davis <seandavi@gmail.com> > >> > Cc: Paul Shannon <pshannon@systemsbiology.org>, bioc > >> > <bioconductor@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.chr 1.hg18.bwa.sorted.bam&locus=chr1:1-1000000<http: www.broadinstitute.o="" rg="" igv="" dynsession="" igv.jnlp?user="anonymous&amp;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@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]]
ADD REPLYlink written 7.6 years ago by Aaron Mackey200
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 >> >> > >> > >> > > >
ADD REPLYlink written 7.6 years ago by Jack Zhu170
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