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Question: TxDb file for Drerio (ie zebrafish)
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gravatar for Brodsky, Michael
4.6 years ago by
Brodsky, Michael10 wrote:
Hi. I am an investigator at the University of Massachusetts Medical School. I've been using the CRISPRseek package written by my colleague Julie Zhu and I'd like to perform searches on the zebrafish genome, but am unable to find a TxDb file for this widely studied organism. Is there a mechanism to request that a TxDb file be prepared for Drerio? Thank you, Mike Brodsky
ADD COMMENTlink modified 4.6 years ago by James W. MacDonald48k • written 4.6 years ago by Brodsky, Michael10
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gravatar for James W. MacDonald
4.6 years ago by
United States
James W. MacDonald48k wrote:
Hi Mike, You don't need to request it. Instead you can make your own. See the help for makeTranscriptDbFromUCSC, in the GenomicFeatures package. Best, Jim On 2/25/2014 11:42 AM, Brodsky, Michael wrote: > Hi. I am an investigator at the University of Massachusetts Medical School. I've been using the CRISPRseek package written by my colleague Julie Zhu and I'd like to perform searches on the zebrafish genome, but am unable to find a TxDb file for this widely studied organism. Is there a mechanism to request that a TxDb file be prepared for Drerio? > > Thank you, > > Mike Brodsky > > _______________________________________________ > 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 University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 4.6 years ago by James W. MacDonald48k
On 02/25/2014 12:20 PM, James W. MacDonald wrote: > Hi Mike, > > You don't need to request it. Instead you can make your own. See the > help for makeTranscriptDbFromUCSC, in the GenomicFeatures package. Yes. It's as easy as library(GenomicFeatures) txdb <- makeTranscriptDbFromUCSC("danRer7", "ensGene") or txdb <- makeTranscriptDbFromUCSC("danRer7", "refGene") depending on whether you want Ensembl or Entrez genes. For both gene models, you'll get a warning that the cds cumulative length is not a multiple of 3 for a lot of transcripts. You might safely ignore if what you do downstream with 'txdb' is not doing anything with the CDS genomic coordinates stored in this TranscriptDb object. Cheers, H. > > Best, > > Jim > > > On 2/25/2014 11:42 AM, Brodsky, Michael wrote: >> Hi. I am an investigator at the University of Massachusetts Medical >> School. I've been using the CRISPRseek package written by my colleague >> Julie Zhu and I'd like to perform searches on the zebrafish genome, >> but am unable to find a TxDb file for this widely studied organism. Is >> there a mechanism to request that a TxDb file be prepared for Drerio? >> >> Thank you, >> >> Mike Brodsky >> >> _______________________________________________ >> 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 > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
ADD REPLYlink written 4.6 years ago by Hervé Pagès ♦♦ 13k
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