[Bioc-devel] request to create BSgenome Bos_taurus_UMD3.1.1
hpages at fredhutch.org
Fri Mar 27 22:25:42 CET 2015
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).
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
>> But I'm getting the same error message...
>> 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)
>  "BSgenome.Btaurus.UCSC.bosTau3"
>  "BSgenome.Btaurus.UCSC.bosTau3.masked"
>  "BSgenome.Btaurus.UCSC.bosTau4"
>  "BSgenome.Btaurus.UCSC.bosTau4.masked"
>  "BSgenome.Btaurus.UCSC.bosTau6"
>  "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:
> (the latest, from 2014/11/25), but bosTau8 is:
> (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
>> Thank you!
>> *Byungkuk Min*
>> Ph.D Candidate
>> University of Science & Technology, <http://ust.ac.kr>
>> Korea Research Institute of Bioscience and Biotechnology
>> 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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