Ha, definitely more than just a 'T'!

Ok, it looks great now! Thanks for the help!


On Fri, Nov 29, 2013 at 3:01 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 11/29/2013 11:18 AM, Brian Smith wrote:
>
>> Thanks Martin. This is what I get:
>>
>> =========
>>  > library(AnnotationHub)
>>  >   hub = AnnotationHub()
>>  >   Mmulatta2 =
>> hub$ensembl.release.72.fasta.macaca_mulatta.dna.Macaca_
>> mulatta.MMUL_1.72.dna.toplevel.fa.rz
>>  >   getSeq(Mmulatta2, GRanges("1", IRanges(567089, width=1)))  #A
>> DNAStringSet
>> instance of length 1
>>    A DNAStringSet instance of length 1
>>      width seq
>>                    names
>> [1]     1 G
>>                    1
>> =========
>>
>> However, if I check against UCSC for this position, it gives a 'G' for
>> rhemac2
>> (2006), but a 'T' for the rhemac3 (2010). So, is this still giving me the
>> old
>> (2006) assembly?
>>
>
> as the path suggests, the genome comes from Ensembl; a little work leads to
>
>   http://www.ensembl.org/Macaca_mulatta/Info/Annotation#assembly
>
> where we're told that this is
>
> Assembly:       MMUL 1.0, Feb 2006
>
> So I guess my original suggestion to use AnnotationHub wasn't helpful in
> this case. Sorry about that, but maybe not all for nothing...
>
> Round 2:
>
> download & uncompress
>
> wget http://hgdownload-test.cse.ucsc.edu/goldenPath/rheMac3/
> bigZips/rheMac3.fa.gz
> gunzip rheMac3.fa.gz
>
> (you could do the above entirely in R with download.file() and
> R.utils::gunzip()) In R re-compress as razip and index (these are both
> relatively lengthy, but need to be done only once).
>
>   library(Rsamtools)
>   razip("rheMac3.fa")
>   indexFa("rheMac3.fa.rz")
>
> use
>
>   fa = FaFile("rheMac3.fa.rz")
>   getSeq(fa, GRanges("1", IRanges(567089, width=1)))
>
> Hopefully you want more than just the 'T'!
>
> Martin
>
>
>> thanks!
>>
>>
>>
>>
>> On Thu, Nov 28, 2013 at 11:52 AM, Martin Morgan <mtmorgan@fhcrc.org
>> <mailto:mtmorgan@fhcrc.org>> wrote:
>>
>>     On 11/28/2013 07:20 AM, Brian Smith wrote:
>>
>>         Hi Martin,
>>
>>         Thanks for the reply!
>>
>>         I get the following:
>>
>>         ------------------------------__--------------------
>>
>>           > library(AnnotationHub)
>>           > hub = AnnotationHub()
>>           > Mmulatta2 =
>>         hub$ensembl.release.73.fasta.__macaca_mulatta.dna.Macaca___
>> mulatta.MMUL_1.73.dna.__toplevel.fa.rz
>>
>>         Warning message:
>>         In .getResource(x, name) : incomplete path
>>
>>
>>     probably you are using a version of R for which this resource is not
>>     available. There is tab completion, and once you get to
>>
>>     hub$ensembl.release.7
>>
>>     press the tab key. Likely you'll see
>>
>>      > hub$ensembl.release.7
>>     hub$ensembl.release.70. ... [427]  hub$ensembl.release.72. ... [393]
>>     hub$ensembl.release.71. ... [426]
>>
>>     and you can complete to
>>
>>     Mmullata2 =
>>     hub$ensembl.release.72.fasta.__macaca_mulatta.dna.Macaca___
>> mulatta.MMUL_1.72.dna.__toplevel.fa.rz
>>
>>
>>     Print Mmullata2 to the console to ensure that it is an 'FaFile'
>> object.
>>
>>
>>           > getSeq(Mmulatta2, GRanges("1", IRanges(567089, width=1)))  #A
>>         DNAStringSet
>>         instance of length 1
>>         Error in (function (classes, fdef, mtable)  :
>>             unable to find an inherited method for function ‘getSeq’ for
>> signature
>>         ‘"character"’
>>
>>         ------------------------------__--------------------
>>
>>
>>         Am I doing something wrong, or do I need to install another
>> package?
>>
>>         thanks!
>>
>>
>>         On Wed, Nov 27, 2013 at 2:33 PM, Martin Morgan <
>> mtmorgan@fhcrc.org
>>         <mailto:mtmorgan@fhcrc.org>
>>         <mailto:mtmorgan@fhcrc.org <mailto:mtmorgan@fhcrc.org>>> wrote:
>>
>>              On 11/27/2013 08:58 AM, Brian Smith wrote:
>>
>>                  Hi,
>>
>>                  I wanted to use the Mmulatta genome in bioconductor, but
>> using
>>                  "available.genomes()", I see that only the rheMac2 (from
>> 2006) is
>>                  available.
>>
>>                  UCSC also shows rheMac3 (from 2010). Is there a way that
>> I can
>>                  download/incorporate this?
>>
>>                  Essentially, I want to find the nucleotide at specific
>>         positions in the
>>                  rhesus genome (e.g. chr1 - 567089).
>>
>>
>>              Depending on what you're actually interested in,
>>
>>                 library(AnnotationHub)
>>                 hub = AnnotationHub()
>>                 Mmulatta =
>>
>>         hub$ensembl.release.73.fasta.____macaca_mulatta.dna.Macaca__
>> ___mulatta.MMUL_1.73.dna.____toplevel.fa.rz
>>
>>
>>
>>              and then
>>
>>               > getSeq(Mmulatta, GRanges("1", IRanges(567089, width=1)))
>>  A
>>         DNAStringSet
>>              instance of length 1
>>                   width seq
>> names
>>              [1]     1 G                                                 1
>>
>>              Martin
>>
>>
>>                  thanks!!
>>
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