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Question: QuasR: how to use an indexed reference genome?
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gravatar for Paul Shannon
4.6 years ago by
Paul Shannon740
Paul Shannon740 wrote:
I am new to QuasR, and alos quite new to aligning short reads to reference genomes more generally. I cannot figure out how to use a pre-built indexed reference genome file with QuasR. The examples supplied with the package work nicely. Scaling up to using all of hg19 raises problems for me. I apologize if I am missing the obvious. To illustrate the problem, I call QuasR's qAlign method with just two arguments (quoting from the man page): sampleFile: a text file listing input sequence files and sample names genome: the reference genome for primary alignments, one of: * a string referring to a "BSgenome" package (e.g. ""BSgenome.Hsapiens.UCSC.hg19""), which will be downloaded automatically from Bioconductor if not present * the name of a fasta sequence file containing one or several sequences (chromosomes) to be used as a reference QuasR apparently invokes the bowtie indexing program when supplied either of the two "genome" options: a BSgenome package, or a fasta file. But since indexing takes a long time -- hours, apparently -- I hoped to provide a ready-made index file, and found some described here: http://bowtie-bio.sourceforge.net/tutorial.shtml specifically ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/hg19.ebwt.zip Various attempts to specify this file, or any of its contents (unzipped) to QuasR fail with these messages: Error: The specified genome /Users/pshannon/s/data/public/bowtie/indexes/hg19.1.ebwt does not have the extension of a fasta file (fa,fasta,fna)> Error: The specified genome has to be a file and not a directory: /Users/pshannon/s/data/public/bowtie/indexes I'll be grateful for advice on how to do this properly. Thanks, - Paul > sessionInfo() R version 3.0.0 (2013-04-03) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] C attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] Rsamtools_1.13.14 BSgenome_1.29.0 Biostrings_2.29.2 QuasR_1.1.4 GenomicRanges_1.13.12 XVector_0.1.0 [7] IRanges_1.19.8 BiocGenerics_0.7.2 Rbowtie_1.1.3 BiocInstaller_1.11.1 loaded via a namespace (and not attached): [1] AnnotationDbi_1.23.11 Biobase_2.21.2 DBI_0.2-7 GenomicFeatures_1.13.8 RCurl_1.95-4.1 [6] RSQLite_0.11.3 ShortRead_1.19.3 XML_3.95-0.2 biomaRt_2.17.0 bitops_1.0-5 [11] compiler_3.0.0 grid_3.0.0 hwriter_1.3 lattice_0.20-15 rtracklayer_1.21.5 [16] stats4_3.0.0 tools_3.0.0 zlibbioc_1.7.0
ADD COMMENTlink modified 4.6 years ago by Michael Stadler310 • written 4.6 years ago by Paul Shannon740
0
gravatar for Michael Stadler
4.6 years ago by
Switzerland
Michael Stadler310 wrote:
Dear Paul, You are right, it is not possibile to use pre-built indices with QuasR, such as those downloaded from the bowtie developers. This is because QuasR needs to be able to go back to the original sequences, for example when working with bisulfite converted reads, which it does by accessing the fasta or BSgenome. Since we cannot control the sequences that went into an externally provided index, it would be more complicated to guarantee a consistent state (identical sequences in BSgenome and index, but also identical sequence names and order, etc.). I do understand that building the index is tedious and will take a few hours, but it has to be done only once, and from there on will be available for futher QuasR analyses. This is still fast compared to the CPU-time that goes into the analysis of most NGS datasets. If more people would prefer to use pre-built indices, and if the BioC agrees to host such big packages, it would also be conceivable to provide index packages corresponding to the BSgenome packages for download. Regards, Michael On 16.05.2013 22:48, Paul Shannon wrote: > I am new to QuasR, and alos quite new to aligning short reads to reference genomes more generally. > I cannot figure out how to use a pre-built indexed reference genome file with QuasR. The examples supplied with the package work nicely. > Scaling up to using all of hg19 raises problems for me. I apologize if I am missing the obvious. > > To illustrate the problem, I call QuasR's qAlign method with just two arguments (quoting from the man page): > > sampleFile: a text file listing input sequence files and sample names > > genome: the reference genome for primary alignments, one of: > > * a string referring to a "BSgenome" package (e.g. > ""BSgenome.Hsapiens.UCSC.hg19""), which will be > downloaded automatically from Bioconductor if not present > > * the name of a fasta sequence file containing one or > several sequences (chromosomes) to be used as a reference > > QuasR apparently invokes the bowtie indexing program when supplied either of the two "genome" options: a BSgenome package, or a fasta file. But since indexing takes a long time -- hours, apparently -- I hoped to provide a ready-made index file, and found some described here: > > > http://bowtie-bio.sourceforge.net/tutorial.shtml > > specifically > > ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/hg19.ebwt.zip > > Various attempts to specify this file, or any of its contents (unzipped) to QuasR fail with these messages: > > > Error: The specified genome /Users/pshannon/s/data/public/bowtie/indexes/hg19.1.ebwt does not have the extension of a fasta file (fa,fasta,fna)> > Error: The specified genome has to be a file and not a directory: /Users/pshannon/s/data/public/bowtie/indexes > > > I'll be grateful for advice on how to do this properly. > > Thanks, > > - Paul > > >> sessionInfo() > R version 3.0.0 (2013-04-03) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] Rsamtools_1.13.14 BSgenome_1.29.0 Biostrings_2.29.2 QuasR_1.1.4 GenomicRanges_1.13.12 XVector_0.1.0 > [7] IRanges_1.19.8 BiocGenerics_0.7.2 Rbowtie_1.1.3 BiocInstaller_1.11.1 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.23.11 Biobase_2.21.2 DBI_0.2-7 GenomicFeatures_1.13.8 RCurl_1.95-4.1 > [6] RSQLite_0.11.3 ShortRead_1.19.3 XML_3.95-0.2 biomaRt_2.17.0 bitops_1.0-5 > [11] compiler_3.0.0 grid_3.0.0 hwriter_1.3 lattice_0.20-15 rtracklayer_1.21.5 > [16] stats4_3.0.0 tools_3.0.0 zlibbioc_1.7.0 > > > >
ADD COMMENTlink written 4.6 years ago by Michael Stadler310
Hi Michael, Thanks for your quick and clarifying response. Since it is not possible to use pre-built indices from the bowtie developers, I would be glad to have a small recipe (perhaps featured prominently in the vignette?) which 1) explains the need for custom-built indices 2) provides (perhaps) a standalone QuasR-specific command for creating one My somewhat fuzzy grasp of the current approach is that 1) QuasR sees the string "BSgenome.Hsapiens.UCSC.hg19" on a call to qAlign 2) QuasR then spends a few hours building a new package with the proper index 3) and saves this package somewhere (I could not figure out where) I agree that a one-time cost to create a QuasR index is quite reasonable, given all the benefits of the package. Maybe it's just my own muddle-headedness, but I could not -- and still cannot :} -- figure out how to do it, where the result is written, and thus how to reuse the index on subsequent runs. Can you give me some assistance? Many thanks, - Paul On May 16, 2013, at 11:41 PM, Michael Stadler wrote: > Dear Paul, > > You are right, it is not possibile to use pre-built indices with QuasR, > such as those downloaded from the bowtie developers. > > This is because QuasR needs to be able to go back to the original > sequences, for example when working with bisulfite converted reads, > which it does by accessing the fasta or BSgenome. Since we cannot > control the sequences that went into an externally provided index, it > would be more complicated to guarantee a consistent state (identical > sequences in BSgenome and index, but also identical sequence names and > order, etc.). > > I do understand that building the index is tedious and will take a few > hours, but it has to be done only once, and from there on will be > available for futher QuasR analyses. This is still fast compared to the > CPU-time that goes into the analysis of most NGS datasets. > > If more people would prefer to use pre-built indices, and if the BioC > agrees to host such big packages, it would also be conceivable to > provide index packages corresponding to the BSgenome packages for download. > > Regards, > Michael > > > > On 16.05.2013 22:48, Paul Shannon wrote: >> I am new to QuasR, and alos quite new to aligning short reads to reference genomes more generally. >> I cannot figure out how to use a pre-built indexed reference genome file with QuasR. The examples supplied with the package work nicely. >> Scaling up to using all of hg19 raises problems for me. I apologize if I am missing the obvious. >> >> To illustrate the problem, I call QuasR's qAlign method with just two arguments (quoting from the man page): >> >> sampleFile: a text file listing input sequence files and sample names >> >> genome: the reference genome for primary alignments, one of: >> >> * a string referring to a "BSgenome" package (e.g. >> ""BSgenome.Hsapiens.UCSC.hg19""), which will be >> downloaded automatically from Bioconductor if not present >> >> * the name of a fasta sequence file containing one or >> several sequences (chromosomes) to be used as a reference >> >> QuasR apparently invokes the bowtie indexing program when supplied either of the two "genome" options: a BSgenome package, or a fasta file. But since indexing takes a long time -- hours, apparently -- I hoped to provide a ready-made index file, and found some described here: >> >> >> http://bowtie-bio.sourceforge.net/tutorial.shtml >> >> specifically >> >> ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/hg19.ebwt.zip >> >> Various attempts to specify this file, or any of its contents (unzipped) to QuasR fail with these messages: >> >> >> Error: The specified genome /Users/pshannon/s/data/public/bowtie/indexes/hg19.1.ebwt does not have the extension of a fasta file (fa,fasta,fna)> >> Error: The specified genome has to be a file and not a directory: /Users/pshannon/s/data/public/bowtie/indexes >> >> >> I'll be grateful for advice on how to do this properly. >> >> Thanks, >> >> - Paul >> >> >>> sessionInfo() >> R version 3.0.0 (2013-04-03) >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> locale: >> [1] C >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] Rsamtools_1.13.14 BSgenome_1.29.0 Biostrings_2.29.2 QuasR_1.1.4 GenomicRanges_1.13.12 XVector_0.1.0 >> [7] IRanges_1.19.8 BiocGenerics_0.7.2 Rbowtie_1.1.3 BiocInstaller_1.11.1 >> >> loaded via a namespace (and not attached): >> [1] AnnotationDbi_1.23.11 Biobase_2.21.2 DBI_0.2-7 GenomicFeatures_1.13.8 RCurl_1.95-4.1 >> [6] RSQLite_0.11.3 ShortRead_1.19.3 XML_3.95-0.2 biomaRt_2.17.0 bitops_1.0-5 >> [11] compiler_3.0.0 grid_3.0.0 hwriter_1.3 lattice_0.20-15 rtracklayer_1.21.5 >> [16] stats4_3.0.0 tools_3.0.0 zlibbioc_1.7.0 >> >> >> >>
ADD REPLYlink written 4.6 years ago by Paul Shannon360
On 05/16/2013 11:41 PM, Michael Stadler wrote: > If more people would prefer to use pre-built indices, and if the BioC > agrees to host such big packages, it would also be conceivable to > provide index packages corresponding to the BSgenome packages for download. We've been experimenting with AnnotationHub (the package, and the cloud resource -- http://bioconductor.org/packages/release/bioc/html/AnnotationHub.html) as a way to provide large(r) data without having to go through the full formalism of creating packages; perhaps the indexes are a good case for this? The user or software would then library(AnnotationHub) hub = AnnotationHub() hub$<tab> ## the preceeding works, now for hypothetical...! hub$bioconductor.QuasR.BSgenome<tab> and when hitting <return> on a complete name the AnnotationHub would do the right thing, downloading and installing the index in an appropriate place (including, e.g., caching in the AnnotationHub cache, if that's appropriate...) Martin -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
ADD REPLYlink written 4.6 years ago by Martin Morgan ♦♦ 21k
Dear Martin, Thank you for pointing out AnnotationHub - it seems that this could indeed be a way to host pre-generated alignment indices. We have internally discussed the option of providing pre-built indices to the community and came to the conclusion that with our current resources, we would not be able to create and maintain the various flavours of indices for current and future BSgenome packages. In addition to the "standard" alignment index, there are two more indices for bisulfite alignments per genome. Furthermore, for each additional aligner supported by QuasR in the future, another set of indices will have to be added. Given that QuasR can generate and re-use those indices locally, we do not consider this a priority. Michael and Dimos On 18.05.2013 02:31, Martin Morgan wrote: > On 05/16/2013 11:41 PM, Michael Stadler wrote: >> If more people would prefer to use pre-built indices, and if the BioC >> agrees to host such big packages, it would also be conceivable to >> provide index packages corresponding to the BSgenome packages for >> download. > > We've been experimenting with AnnotationHub (the package, and the cloud > resource -- > http://bioconductor.org/packages/release/bioc/html/AnnotationHub.html) > as a way to provide large(r) data without having to go through the full > formalism of creating packages; perhaps the indexes are a good case for > this? The user or software would then > > library(AnnotationHub) > hub = AnnotationHub() > hub$<tab> > ## the preceeding works, now for hypothetical...! > hub$bioconductor.QuasR.BSgenome<tab> > > and when hitting <return> on a complete name the AnnotationHub would do > the right thing, downloading and installing the index in an appropriate > place (including, e.g., caching in the AnnotationHub cache, if that's > appropriate...) > > Martin > -- -------------------------------------------- Michael Stadler, PhD Head of Computational Biology Friedrich Miescher Institute Basel (Switzerland) Phone : +41 61 697 6492 Fax : +41 61 697 3976 Mail : michael.stadler at fmi.ch
ADD REPLYlink written 4.6 years ago by Michael Stadler310
0
gravatar for Michael Stadler
4.6 years ago by
Switzerland
Michael Stadler310 wrote:
Hi Paul, Please find my answers below: On 17.05.2013 15:01, Paul Shannon wrote: > Hi Michael, > > Thanks for your quick and clarifying response. > > Since it is not possible to use pre-built indices from the bowtie developers, I would be glad to have a small recipe (perhaps featured prominently in the vignette?) which > > 1) explains the need for custom-built indices > 2) provides (perhaps) a standalone QuasR-specific command for creating one It is actually much simpler than you expect: qAlign() creates the index automatically if it does not yet exist. The index is then saved in a default location (as a new R package if your reference is a BSgenome, or else in the same directory containing the fasta reference), and will be automatically re-used when qAlign is called with the same reference. > My somewhat fuzzy grasp of the current approach is that > > 1) QuasR sees the string "BSgenome.Hsapiens.UCSC.hg19" on a call to qAlign > 2) QuasR then spends a few hours building a new package with the proper index Yes, this is described in section 5.3 of the vignette. > 3) and saves this package somewhere (I could not figure out where) This is described in the documentation to qAlign. I agree that it would be better to have this all described more explicitly in a single place, so I added a description to the qAlign documentation (available shortly in the development branch). I hope this makes it all clear. Best, Michael
ADD COMMENTlink written 4.6 years ago by Michael Stadler310
Thanks, Michael. May I cast my one vote, as a new user of Quasr, for an extra measure of transparency? I have lost a few days to my confusion. My reasoning -- which might be idiosyncratic, and which you may find unconvincing -- is that if qAlign, in some invocations (but not all) needs to spend a few hours creating an index, and writes it to a place which is not entirely obvious (lib.loc), then I as a user am mightily confused. As I have been! :} I would have been much better off if qAlign had told me: 1) you specified a genome package by name for your reference 2) in order to use that, qAlign needs for it to be indexed 3) we cannot find an indexed version of that genome in your R library or any lib.loc directory 4) please specify an alternative lib.loc, and explicit path, or? 5) create a new index for your genome using this command: buildIndexAsPackage(genomePackageName, destinationDir) # or some such method call 6) you can then specify that newly-built index package in subsequent calls to qAlign this way: qAlign(samplesFile, genome="~/path/to/genome-index- package.tar.gz") - Paul On May 17, 2013, at 6:59 AM, Michael Stadler wrote: > Hi Paul, > > Please find my answers below: > > On 17.05.2013 15:01, Paul Shannon wrote: >> Hi Michael, >> >> Thanks for your quick and clarifying response. >> >> Since it is not possible to use pre-built indices from the bowtie developers, I would be glad to have a small recipe (perhaps featured prominently in the vignette?) which >> >> 1) explains the need for custom-built indices >> 2) provides (perhaps) a standalone QuasR-specific command for creating one > It is actually much simpler than you expect: qAlign() creates the index > automatically if it does not yet exist. The index is then saved in a > default location (as a new R package if your reference is a BSgenome, or > else in the same directory containing the fasta reference), and will be > automatically re-used when qAlign is called with the same reference. > >> My somewhat fuzzy grasp of the current approach is that >> >> 1) QuasR sees the string "BSgenome.Hsapiens.UCSC.hg19" on a call to qAlign >> 2) QuasR then spends a few hours building a new package with the proper index > Yes, this is described in section 5.3 of the vignette. > >> 3) and saves this package somewhere (I could not figure out where) > This is described in the documentation to qAlign. I agree that it would > be better to have this all described more explicitly in a single place, > so I added a description to the qAlign documentation (available shortly > in the development branch). > > I hope this makes it all clear. > > Best, > Michael >
ADD REPLYlink written 4.6 years ago by Paul Shannon360
same here, I would like to use QuasR more often, the reason I use Rsubread (instead of say gmapR or quasR) is simply that I know where my indexed genomes are and how to regenerate them if need be this is a big deal for lazy people like me ;-) On Fri, May 17, 2013 at 7:51 AM, Paul Shannon < paul.thurmond.shannon@gmail.com> wrote: > Thanks, Michael. > > May I cast my one vote, as a new user of Quasr, for an extra measure of > transparency? I have lost a few days to my confusion. > > My reasoning -- which might be idiosyncratic, and which you may find > unconvincing -- is that if qAlign, in some invocations (but not all) needs > to spend a few hours creating an index, and writes it to a place which is > not entirely obvious (lib.loc), then I as a user am mightily confused. As > I have been! :} > > I would have been much better off if qAlign had told me: > > 1) you specified a genome package by name for your reference > 2) in order to use that, qAlign needs for it to be indexed > 3) we cannot find an indexed version of that genome in your R library or > any lib.loc directory > 4) please specify an alternative lib.loc, and explicit path, or > 5) create a new index for your genome using this command: > buildIndexAsPackage(genomePackageName, destinationDir) # or some > such method call > 6) you can then specify that newly-built index package in subsequent > calls to qAlign this way: > qAlign(samplesFile, genome="~/path/to/genome-index- package.tar.gz") > > - Paul > > On May 17, 2013, at 6:59 AM, Michael Stadler wrote: > > > Hi Paul, > > > > Please find my answers below: > > > > On 17.05.2013 15:01, Paul Shannon wrote: > >> Hi Michael, > >> > >> Thanks for your quick and clarifying response. > >> > >> Since it is not possible to use pre-built indices from the bowtie > developers, I would be glad to have a small recipe (perhaps featured > prominently in the vignette?) which > >> > >> 1) explains the need for custom-built indices > >> 2) provides (perhaps) a standalone QuasR-specific command for creating > one > > It is actually much simpler than you expect: qAlign() creates the index > > automatically if it does not yet exist. The index is then saved in a > > default location (as a new R package if your reference is a BSgenome, or > > else in the same directory containing the fasta reference), and will be > > automatically re-used when qAlign is called with the same reference. > > > >> My somewhat fuzzy grasp of the current approach is that > >> > >> 1) QuasR sees the string "BSgenome.Hsapiens.UCSC.hg19" on a call to > qAlign > >> 2) QuasR then spends a few hours building a new package with the > proper index > > Yes, this is described in section 5.3 of the vignette. > > > >> 3) and saves this package somewhere (I could not figure out where) > > This is described in the documentation to qAlign. I agree that it would > > be better to have this all described more explicitly in a single place, > > so I added a description to the qAlign documentation (available shortly > > in the development branch). > > > > I hope this makes it all clear. > > > > Best, > > Michael > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]
ADD REPLYlink written 4.6 years ago by Tim Triche4.2k
Dear Paul and Tim, It was our intention that lazy people (including ourselves) do not have to worry about index generation. Contrary to what you write, Paul, it is however not true that QuasR will build the genome index without informing the user. In such cases, it says: alignment files missing - need to: create alignment index for the genome [...] and gives you a countdown of 10 seconds, during which you can interrupt the process if it is not what you intended. As mentioned before, we have added a paragraph to the qAlign documentation detailing the storage location of that index, which you can fully control. The major reason for the current interface design is that QuasR must retain a consistent state of your project, and prevent users from unintentionally mixing incompatible genome sequence and aligner index. This seems to be contrary to your expectations, maybe because current aligners require genome indices explicitly. We believe that for most (less experienced) users, it is safer and more comfortable to let QuasR hide some of the technical details underneath its cover. We consciously chose this design, which allows even users who don't know that the genome needs to be indexed, or how this needs to be done, to safely use QuasR. This creates an additional layer of abstraction compared to a direct analysis, e.g. on the command line. For users preferring to explicitly specify *how* things should be done, rather than *what* should be done, QuasR might not be the right tool. - Michael and Dimos On 18.05.2013 01:53, Tim Triche, Jr. wrote: > same here, I would like to use QuasR more often, the reason I use > Rsubread (instead of say gmapR or quasR) is simply that I know where my > indexed genomes are and how to regenerate them if need be > > this is a big deal for lazy people like me ;-) > > > > On Fri, May 17, 2013 at 7:51 AM, Paul Shannon > <paul.thurmond.shannon at="" gmail.com=""> <mailto:paul.thurmond.shannon at="" gmail.com="">> wrote: > > Thanks, Michael. > > May I cast my one vote, as a new user of Quasr, for an extra measure > of transparency? I have lost a few days to my confusion. > > My reasoning -- which might be idiosyncratic, and which you may find > unconvincing -- is that if qAlign, in some invocations (but not all) > needs to spend a few hours creating an index, and writes it to a > place which is not entirely obvious (lib.loc), then I as a user am > mightily confused. As I have been! :} > > I would have been much better off if qAlign had told me: > > 1) you specified a genome package by name for your reference > 2) in order to use that, qAlign needs for it to be indexed > 3) we cannot find an indexed version of that genome in your R > library or any lib.loc directory > 4) please specify an alternative lib.loc, and explicit path, or? > 5) create a new index for your genome using this command: > buildIndexAsPackage(genomePackageName, destinationDir) # or > some such method call > 6) you can then specify that newly-built index package in > subsequent calls to qAlign this way: > qAlign(samplesFile, > genome="~/path/to/genome-index-package.tar.gz") > > - Paul > > On May 17, 2013, at 6:59 AM, Michael Stadler wrote: > > > Hi Paul, > > > > Please find my answers below: > > > > On 17.05.2013 15:01, Paul Shannon wrote: > >> Hi Michael, > >> > >> Thanks for your quick and clarifying response. > >> > >> Since it is not possible to use pre-built indices from the bowtie > developers, I would be glad to have a small recipe (perhaps featured > prominently in the vignette?) which > >> > >> 1) explains the need for custom-built indices > >> 2) provides (perhaps) a standalone QuasR-specific command for > creating one > > It is actually much simpler than you expect: qAlign() creates the > index > > automatically if it does not yet exist. The index is then saved in a > > default location (as a new R package if your reference is a > BSgenome, or > > else in the same directory containing the fasta reference), and > will be > > automatically re-used when qAlign is called with the same reference. > > > >> My somewhat fuzzy grasp of the current approach is that > >> > >> 1) QuasR sees the string "BSgenome.Hsapiens.UCSC.hg19" on a call > to qAlign > >> 2) QuasR then spends a few hours building a new package with the > proper index > > Yes, this is described in section 5.3 of the vignette. > > > >> 3) and saves this package somewhere (I could not figure out where) > > This is described in the documentation to qAlign. I agree that it > would > > be better to have this all described more explicitly in a single > place, > > so I added a description to the qAlign documentation (available > shortly > > in the development branch). > > > > I hope this makes it all clear. > > > > Best, > > Michael > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > -- > /A model is a lie that helps you see the truth./ > / > / > Howard Skipper > <http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> -- -------------------------------------------- Michael Stadler, PhD Head of Computational Biology Friedrich Miescher Institute Basel (Switzerland) Phone : +41 61 697 6492 Fax : +41 61 697 3976 Mail : michael.stadler at fmi.ch
ADD REPLYlink written 4.6 years ago by Michael Stadler310
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