a question about girafe
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chunjiang he ▴ 80
@chunjiang-he-3439
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Hi, Does anybody use girafe to analyze .sam file extracting from bowtie. Some example is better. thanks so much, Jiang [[alternative HTML version deleted]]
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@sean-davis-490
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On Fri, Jul 1, 2011 at 6:14 PM, chun-jiang he <camelbbs at="" gmail.com=""> wrote: > Hi, > > Does anybody use girafe to analyze .sam file extracting from bowtie. > > Some example is better. Hi, Jiang. Have you looked at the vignette for the girafe package? http://www.bioconductor.org/packages/release/bioc/vignettes/girafe/ins t/doc/girafe.pdf It does include examples. If you have problems, send the code that you have tried, the error messages, and the output of sessionInfo(). Sean > thanks so much, > > Jiang > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Thanks Sean. But I dont know where I can input my .sam file. On Fri, Jul 1, 2011 at 9:48 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > On Fri, Jul 1, 2011 at 6:14 PM, chun-jiang he <camelbbs@gmail.com> wrote: > > Hi, > > > > Does anybody use girafe to analyze .sam file extracting from bowtie. > > > > Some example is better. > > Hi, Jiang. Have you looked at the vignette for the girafe package? > > > http://www.bioconductor.org/packages/release/bioc/vignettes/girafe/i nst/doc/girafe.pdf > > It does include examples. If you have problems, send the code that > you have tried, the error messages, and the output of sessionInfo(). > > Sean > > > > thanks so much, > > > > Jiang > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > 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 > > > [[alternative HTML version deleted]]
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On Fri, Jul 1, 2011 at 10:55 PM, chun-jiang he <camelbbs at="" gmail.com=""> wrote: > Thanks Sean. But I dont know where I can input my .sam file. Well, you'll want to convert your .sam file to a sorted .bam file and then index the .bam file (use samtools to do that, for instance). Then, you can use the readAligned() function from the ShortRead package. In the girafe vignette, you can see section 2.2 for an example. Sean > On Fri, Jul 1, 2011 at 9:48 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > >> On Fri, Jul 1, 2011 at 6:14 PM, chun-jiang he <camelbbs at="" gmail.com=""> wrote: >> > Hi, >> > >> > Does anybody use girafe to analyze .sam file extracting from bowtie. >> > >> > Some example is better. >> >> Hi, Jiang. ?Have you looked at the vignette for the girafe package? >> >> >> http://www.bioconductor.org/packages/release/bioc/vignettes/girafe/ inst/doc/girafe.pdf >> >> It does include examples. ?If you have problems, send the code that >> you have tried, the error messages, and the output of sessionInfo(). >> >> Sean >> >> >> > thanks so much, >> > >> > Jiang >> > >> > ? ? ? ?[[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor at r-project.org >> > 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 at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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On 07/01/2011 08:01 PM, Sean Davis wrote: > On Fri, Jul 1, 2011 at 10:55 PM, chun-jiang he<camelbbs at="" gmail.com=""> wrote: >> Thanks Sean. But I dont know where I can input my .sam file. > > Well, you'll want to convert your .sam file to a sorted .bam file and > then index the .bam file (use samtools to do that, for instance). or Rsamtools asBam, sortBam, indexBam which are simple wrappers around samtools code so have the same basic memory / speed characteristics. Martin > Then, you can use the readAligned() function from the ShortRead > package. In the girafe vignette, you can see section 2.2 for an > example. > > Sean > > >> On Fri, Jul 1, 2011 at 9:48 PM, Sean Davis<sdavis2 at="" mail.nih.gov=""> wrote: >> >>> On Fri, Jul 1, 2011 at 6:14 PM, chun-jiang he<camelbbs at="" gmail.com=""> wrote: >>>> Hi, >>>> >>>> Does anybody use girafe to analyze .sam file extracting from bowtie. >>>> >>>> Some example is better. >>> >>> Hi, Jiang. Have you looked at the vignette for the girafe package? >>> >>> >>> http://www.bioconductor.org/packages/release/bioc/vignettes/girafe /inst/doc/girafe.pdf >>> >>> It does include examples. If you have problems, send the code that >>> you have tried, the error messages, and the output of sessionInfo(). >>> >>> Sean >>> >>> >>>> thanks so much, >>>> >>>> Jiang >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> 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 at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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Hi, Thanks. There is an error when I run readAligned(). I have converted .sam to .bam and sorted indexed it. I got two files as sorted.bam and sorted.bam.bai > exA<-readAligned(dirPath="~",type="Bowtie", + pattern="SRR032476-sorted.bam") Error: Input/Output 'readAligned' failed to parse files dirPath: '~' pattern: 'SRR032476-sorted.bam' type: 'Bowtie' error: incorrect number of fields (1) /cchome/che/SRR032476-sorted.bam:1 Jiang On Sun, Jul 3, 2011 at 7:09 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > On 07/01/2011 08:01 PM, Sean Davis wrote: > >> On Fri, Jul 1, 2011 at 10:55 PM, chun-jiang he<camelbbs@gmail.com> >> wrote: >> >>> Thanks Sean. But I dont know where I can input my .sam file. >>> >> >> Well, you'll want to convert your .sam file to a sorted .bam file and >> then index the .bam file (use samtools to do that, for instance). >> > > or Rsamtools asBam, sortBam, indexBam which are simple wrappers around > samtools code so have the same basic memory / speed characteristics. > > Martin > > > Then, you can use the readAligned() function from the ShortRead >> package. In the girafe vignette, you can see section 2.2 for an >> example. >> >> Sean >> >> >> On Fri, Jul 1, 2011 at 9:48 PM, Sean Davis<sdavis2@mail.nih.gov> wrote: >>> >>> On Fri, Jul 1, 2011 at 6:14 PM, chun-jiang he<camelbbs@gmail.com> >>>> wrote: >>>> >>>>> Hi, >>>>> >>>>> Does anybody use girafe to analyze .sam file extracting from bowtie. >>>>> >>>>> Some example is better. >>>>> >>>> >>>> Hi, Jiang. Have you looked at the vignette for the girafe package? >>>> >>>> >>>> http://www.bioconductor.org/**packages/release/bioc/** >>>> vignettes/girafe/inst/doc/**girafe.pdf<http: www.bioconductor.or="" g="" packages="" release="" bioc="" vignettes="" girafe="" inst="" doc="" girafe.pdf=""> >>>> >>>> It does include examples. If you have problems, send the code that >>>> you have tried, the error messages, and the output of sessionInfo(). >>>> >>>> Sean >>>> >>>> >>>> thanks so much, >>>>> >>>>> Jiang >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> ______________________________**_________________ >>>>> Bioconductor mailing list >>>>> Bioconductor@r-project.org >>>>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: sta="" t.ethz.ch="" mailman="" listinfo="" bioconductor=""> >>>>> Search the archives: >>>>> >>>> http://news.gmane.org/gmane.**science.biology.informatics.**condu ctor<http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> >>>> >>>>> >>>>> >>>> >>> [[alternative HTML version deleted]] >>> >>> ______________________________**_________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.="" ethz.ch="" mailman="" listinfo="" bioconductor=""> >>> Search the archives: http://news.gmane.org/gmane.** >>> science.biology.informatics.**conductor<http: news.gmane.org="" gman="" e.science.biology.informatics.conductor=""> >>> >>> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 > [[alternative HTML version deleted]]
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On Tue, Jul 5, 2011 at 11:11 AM, chun-jiang he <camelbbs at="" gmail.com=""> wrote: > Hi, > Thanks. There is an error when I run readAligned(). I have converted .sam to > .bam and sorted indexed it. I got two files as sorted.bam and sorted.bam.bai >> exA<-readAligned(dirPath="~",type="Bowtie", > + pattern="SRR032476-sorted.bam") > Error: Input/Output > ? 'readAligned' failed to parse files > ? dirPath: '~' > ? pattern: 'SRR032476-sorted.bam' > ? type: 'Bowtie' > ? error: incorrect number of fields (1) /cchome/che/SRR032476-sorted.bam:1 Looks like you specified type="Bowtie". You have a bam file, not a bowtie-formatted file. Have a look at the help for readAligned() to get a list of available types. Sean > Jiang > On Sun, Jul 3, 2011 at 7:09 AM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: >> >> On 07/01/2011 08:01 PM, Sean Davis wrote: >>> >>> On Fri, Jul 1, 2011 at 10:55 PM, chun-jiang he<camelbbs at="" gmail.com=""> >>> ?wrote: >>>> >>>> Thanks Sean. But I dont know where I can input my .sam file. >>> >>> Well, you'll want to convert your .sam file to a sorted .bam file and >>> then index the .bam file (use samtools to do that, for instance). >> >> or Rsamtools asBam, sortBam, indexBam which are simple wrappers around >> samtools code so have the same basic memory / speed characteristics. >> >> Martin >> >>> Then, you can use the readAligned() function from the ShortRead >>> package. ?In the girafe vignette, you can see section 2.2 for an >>> example. >>> >>> Sean >>> >>> >>>> On Fri, Jul 1, 2011 at 9:48 PM, Sean Davis<sdavis2 at="" mail.nih.gov=""> ?wrote: >>>> >>>>> On Fri, Jul 1, 2011 at 6:14 PM, chun-jiang he<camelbbs at="" gmail.com=""> >>>>> ?wrote: >>>>>> >>>>>> Hi, >>>>>> >>>>>> Does anybody use girafe to analyze .sam file extracting from bowtie. >>>>>> >>>>>> Some example is better. >>>>> >>>>> Hi, Jiang. ?Have you looked at the vignette for the girafe package? >>>>> >>>>> >>>>> >>>>> http://www.bioconductor.org/packages/release/bioc/vignettes/gira fe/inst/doc/girafe.pdf >>>>> >>>>> It does include examples. ?If you have problems, send the code that >>>>> you have tried, the error messages, and the output of sessionInfo(). >>>>> >>>>> Sean >>>>> >>>>> >>>>>> thanks so much, >>>>>> >>>>>> Jiang >>>>>> >>>>>> ? ? ? ?[[alternative HTML version deleted]] >>>>>> >>>>>> _______________________________________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor at r-project.org >>>>>> 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 at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> -- >> Computational Biology >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 >> >> Location: M1-B861 >> Telephone: 206 667-2793 > >
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Hello, note that package "girafe" also contains a function called "agiFromBam" which directly reads in sorted and indexed BAM files into an object of the AlignedGenomeIntervals class. This function also relies on functionalities of the Rsamtools package but should be faster and more memory-efficient than first using "readAligned" and then converting the result into an AlignedGenomeIntervals object. Please let me know if there are any issues with that function. Cheers, Joern On 07/05/2011 05:36 PM, Sean Davis wrote: > On Tue, Jul 5, 2011 at 11:11 AM, chun-jiang he<camelbbs at="" gmail.com=""> wrote: >> Hi, >> Thanks. There is an error when I run readAligned(). I have converted .sam to >> .bam and sorted indexed it. I got two files as sorted.bam and sorted.bam.bai >>> exA<-readAligned(dirPath="~",type="Bowtie", >> + pattern="SRR032476-sorted.bam") >> Error: Input/Output >> 'readAligned' failed to parse files >> dirPath: '~' >> pattern: 'SRR032476-sorted.bam' >> type: 'Bowtie' >> error: incorrect number of fields (1) /cchome/che/SRR032476-sorted.bam:1 > Looks like you specified type="Bowtie". You have a bam file, not a > bowtie-formatted file. Have a look at the help for readAligned() to > get a list of available types. > > Sean > > -- Joern Toedling, PhD Core Facility Bioinformatics Institute of Molecular Biology gGmbH (IMB) http://www.imb-mainz.de Tel.: +49 6131 39 21511
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