[Bioc-devel] request to create BSgenome Bos_taurus_UMD3.1.1

[Hervé Pagès]

So I went ahead and did BSgenome.Btaurus.UCSC.bosTau8. It should
become available via biocLite() in the next couple of hours (in
BioC devel only).

H.

On 03/26/2015 12:54 AM, Hervé Pagès wrote:
> Hi Byungkuk,
>
> On 03/25/2015 10:17 PM, Byungkuk Min wrote:
>> Dear Dr.Pages,
>>
>> I've been trying to build a BSgenome for Bos_taurus_UMD3.1.1 from NCBI
>> <http://www.ncbi.nlm.nih.gov/assembly/GCF_000003055.6/>.
>> But I'm getting the same error message...
>>
>>> library(BSgenome)
>>> forgeBSgenomeDataPkg("/PATH/TO/genome.fa")
>> Error: Line starting '>1 ...' is malformed!
>>
>> I don't have much knowledge of R, so creating a custom BSgenome seems out
>> of my league.
>>
>> I would like to kindly request the bovine BSgenome package.
>
> Do you really need *that* particular assembly (GCF_000003055.6).
> Otherwise, there are already some bovine BSgenome packages available:
>
>    > library(BSgenome)
>    > grep("Btaurus", available.genomes(), value=TRUE)
>    [1] "BSgenome.Btaurus.UCSC.bosTau3"
>    [2] "BSgenome.Btaurus.UCSC.bosTau3.masked"
>    [3] "BSgenome.Btaurus.UCSC.bosTau4"
>    [4] "BSgenome.Btaurus.UCSC.bosTau4.masked"
>    [5] "BSgenome.Btaurus.UCSC.bosTau6"
>    [6] "BSgenome.Btaurus.UCSC.bosTau6.masked"
>
> We don't have bosTau8 yet, which is the latest bovine assembly available
> at UCSC (they added it in June 2014) but I could add it. Note that
> despite its name (also Bos_taurus_UMD_3.1.1), bosTau8 is not the same
> assembly as the one you picked up on NCBI. Yours is:
>
>    http://www.ncbi.nlm.nih.gov/assembly/GCF_000003055.6
>
> (the latest, from 2014/11/25), but bosTau8 is:
>
>    http://www.ncbi.nlm.nih.gov/assembly/GCF_000003055.5
>
> (much older, from 2009/12/01)
>
> Anyway, if we ignore chrM and the thousands of scaffolds that are
> included in these assemblies, the sequences of the "main" chromosomes
> (i.e. chr1 to chr29 + chrX) are exactly the same in the 2 assemblies.
>
> So maybe the BSgenome package for bosTau8 will do?
>
> Note that the main advantage of making a BSgenome package for a
> UCSC assembly (instead of using an NCBI assembly) is that the BSgenome
> object then interoperates nicely with the TxDb object that one can
> easily make from one of the UCSC tracks available for that assembly
> (using the makeTxDbFromUCSC() function from the GenomicFeatures
> package).
>
> H.
>
>>
>> Thank you!
>>
>>
>>
>>
>> *Byungkuk Min*
>> Ph.D Candidate
>> University of Science & Technology, <http://ust.ac.kr>
>> Korea Research Institute of Bioscience and Biotechnology
>> <http://www.kribb.re.kr>
>> 125 Gwahangno, Yuseong-Gu, Daejeon, Korea (305-806)
>> Laboratory : 042-860-4423
>> FAX : 042-860-4608
>> Cell phone : 010-5209-7377
>>
>>     [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
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>>
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
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