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Question: Get all 3'utr and 5'utr region from GenomicFeatures
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gravatar for Fabrice Tourre
6.5 years ago by
Fabrice Tourre950 wrote:
Dear list, How can I get all 3'utr and 5'utr region from GenomicFeatures of Human? There are fiveUTRsByTranscript, threeUTRsByTranscript methods in GenomicFeatures. But how can I get these regions? Thanks.
ADD COMMENTlink modified 6.5 years ago by James W. MacDonald45k • written 6.5 years ago by Fabrice Tourre950
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gravatar for James W. MacDonald
6.5 years ago by
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James W. MacDonald45k wrote:
Hi Fabrice, On 5/24/2011 4:56 AM, Fabrice Tourre wrote: > Dear list, > > How can I get all 3'utr and 5'utr region from GenomicFeatures of Human? > There are fiveUTRsByTranscript, threeUTRsByTranscript methods in > GenomicFeatures. But how can I get these regions? hg19 <- makeFeatureDbFromUCSC(genome = "hg19", table = "refGene") utr3 <- threeUTRsByTranscript(ref19) Which seems pretty obvious to me, given the help pages for these functions. It would be helpful if you could give us an indication of where you got stuck, and what in particular you didn't understand from the help pages, so we can improve our documentation. Best, Jim > > Thanks. > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
ADD COMMENTlink written 6.5 years ago by James W. MacDonald45k
Hi, On Tue, May 24, 2011 at 9:18 AM, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: > Hi Fabrice, > > On 5/24/2011 4:56 AM, Fabrice Tourre wrote: >> >> Dear list, >> >> How can I get all 3'utr and 5'utr region from GenomicFeatures of Human? >> There are fiveUTRsByTranscript, threeUTRsByTranscript methods in >> GenomicFeatures. But how can I get these regions? > > hg19 <- makeFeatureDbFromUCSC(genome = "hg19", table = "refGene") > utr3 <- threeUTRsByTranscript(ref19) > > Which seems pretty obvious to me, given the help pages for these functions. > > It would be helpful if you could give us an indication of where you got > stuck, and what in particular you didn't understand from the help pages, so > we can improve our documentation. Perhaps the OP wanted to know how to get the sequences from those regions, given the results from those functions? If that's the case, I'd load up the BSgenome.Hsapiens.UCSC.hg19 library, iterate over my results one chromosome at a time, and use a mix of the Views function over the unmasked chromosome (using ranges across the 3'utr across the chromosome as the second argument) ... you'll have to take care of seqs on the reverse strand. You could also look at the getSeq function. I'lll leave the actual writing of the code as an exercise to the reader since I think it's useful to know how Views work and you'll have to read up on the documentation a bit :-) -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
ADD REPLYlink written 6.5 years ago by Steve Lianoglou12k
Steve, It make sense. Thank you very much. On Tue, May 24, 2011 at 5:19 PM, Steve Lianoglou <mailinglist.honeypot at="" gmail.com=""> wrote: > Hi, > > On Tue, May 24, 2011 at 9:18 AM, James W. MacDonald > <jmacdon at="" med.umich.edu=""> wrote: >> Hi Fabrice, >> >> On 5/24/2011 4:56 AM, Fabrice Tourre wrote: >>> >>> Dear list, >>> >>> How can I get all 3'utr and 5'utr region from GenomicFeatures of Human? >>> There are fiveUTRsByTranscript, threeUTRsByTranscript methods in >>> GenomicFeatures. But how can I get these regions? >> >> hg19 <- makeFeatureDbFromUCSC(genome = "hg19", table = "refGene") >> utr3 <- threeUTRsByTranscript(ref19) >> >> Which seems pretty obvious to me, given the help pages for these functions. >> >> It would be helpful if you could give us an indication of where you got >> stuck, and what in particular you didn't understand from the help pages, so >> we can improve our documentation. > > Perhaps the OP wanted to know how to get the sequences from those > regions, given the results from those functions? > > If that's the case, I'd load up the BSgenome.Hsapiens.UCSC.hg19 > library, iterate over my results one chromosome at a time, and use a > mix of the Views function over the unmasked chromosome (using ranges > across the 3'utr across the chromosome as the second argument) ... > you'll have to take care of seqs on the reverse strand. > > You could also look at the getSeq function. > > I'lll leave the actual writing of the code as an exercise to the > reader since I think it's useful to know how Views work and you'll > have to read up on the documentation a bit :-) > > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > ?| Memorial Sloan-Kettering Cancer Center > ?| Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > > _______________________________________________ > 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 >
ADD REPLYlink written 6.5 years ago by Fabrice Tourre950
Hi, On Tue, May 24, 2011 at 11:34 AM, Fabrice Tourre <fabrice.ciup at="" gmail.com=""> wrote: > Steve, > > It make sense. > > Thank you very much. Nice -- one last thing. If you will be taking the Views route, read through this recent thread from the bioc-sig-seq mailing list: https://stat.ethz.ch/pipermail/bioc-sig- sequencing/2011-May/001985.html In particular this (very detailed) explanation from Herve about when/how you might want to use compact with Views so that you don't end up trying to store your entire genome in RAM: https://stat.ethz.ch/pipermail/bioc-sig- sequencing/2011-May/002000.html Hope that helps, -steve > > On Tue, May 24, 2011 at 5:19 PM, Steve Lianoglou > <mailinglist.honeypot at="" gmail.com=""> wrote: >> Hi, >> >> On Tue, May 24, 2011 at 9:18 AM, James W. MacDonald >> <jmacdon at="" med.umich.edu=""> wrote: >>> Hi Fabrice, >>> >>> On 5/24/2011 4:56 AM, Fabrice Tourre wrote: >>>> >>>> Dear list, >>>> >>>> How can I get all 3'utr and 5'utr region from GenomicFeatures of Human? >>>> There are fiveUTRsByTranscript, threeUTRsByTranscript methods in >>>> GenomicFeatures. But how can I get these regions? >>> >>> hg19 <- makeFeatureDbFromUCSC(genome = "hg19", table = "refGene") >>> utr3 <- threeUTRsByTranscript(ref19) >>> >>> Which seems pretty obvious to me, given the help pages for these functions. >>> >>> It would be helpful if you could give us an indication of where you got >>> stuck, and what in particular you didn't understand from the help pages, so >>> we can improve our documentation. >> >> Perhaps the OP wanted to know how to get the sequences from those >> regions, given the results from those functions? >> >> If that's the case, I'd load up the BSgenome.Hsapiens.UCSC.hg19 >> library, iterate over my results one chromosome at a time, and use a >> mix of the Views function over the unmasked chromosome (using ranges >> across the 3'utr across the chromosome as the second argument) ... >> you'll have to take care of seqs on the reverse strand. >> >> You could also look at the getSeq function. >> >> I'lll leave the actual writing of the code as an exercise to the >> reader since I think it's useful to know how Views work and you'll >> have to read up on the documentation a bit :-) >> >> -steve >> >> -- >> Steve Lianoglou >> Graduate Student: Computational Systems Biology >> ?| Memorial Sloan-Kettering Cancer Center >> ?| Weill Medical College of Cornell University >> Contact Info: http://cbio.mskcc.org/~lianos/contact >> >> _______________________________________________ >> 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 >> > -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
ADD REPLYlink written 6.5 years ago by Steve Lianoglou12k
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