[BioC] TxDb file for Drerio (ie zebrafish)

[Hervé Pagès]

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