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