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!! >> >> [[alternative HTML version deleted]] >> >> ___________________________________________________ >> >> Bioconductor mailing list >> Bioconductor@r-project.org <mailto:bioconductor@r-project.org> >> <mailto:bioconductor@r-__project.org <mailto:bioconductor@r-="">> project.org>> >> https://stat.ethz.ch/mailman/____listinfo/bioconductor >> <https: stat.ethz.ch="" mailman="" __listinfo="" bioconductor=""> >> >> >> <https: stat.ethz.ch="" mailman="" __listinfo="" bioconductor="">> <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">> >> Search the archives: >> http://news.gmane.org/gmane.____science.biology.informatics. >> ____conductor <http: news.gmane.org="" gmane._="">> _science.biology.informatics.__conductor> >> >> >> >> <http: news.gmane.org="" gmane.__science.biology.informatics._="">> _conductor >> <http: news.gmane.org="" gmane.science.biology.informatics.="">> conductor>> >> >> >> >> -- >> Computational Biology / Fred Hutchinson Cancer Research >> Center >> 1100 Fairview Ave. N. >> PO Box 19024 Seattle, WA 98109 >> >> Location: Arnold Building M1 B861 >> Phone: (206) 667-2793 <tel:%28206%29%20667-2793> >> <tel:%28206%29%20667-2793> >> >> >> >> >> -- >> Computational Biology / Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N. >> PO Box 19024 Seattle, WA 98109 >> >> Location: Arnold Building M1 B861 >> Phone: (206) 667-2793 <tel:%28206%29%20667-2793> >> >> >> > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > [[alternative HTML version deleted]]