I'm not so sure the shift operator will do the trick since we don't have a mapping of Ensembl transcripts to UCSC known gene transcripts. Also what is stored in the SimpleRleList object. Are the elements transcripts and do the values represent coverage?
Patrick On 3/16/10 1:53 PM, Michael Lawrence wrote: > So to summarize, Jason needs to use GenomicFeatures to get the ensembl > exons out, get the start positions, and use them to shift his ranges. > > On Tue, Mar 16, 2010 at 1:37 PM, Patrick Aboyoun <[email protected] > <mailto:[email protected]>> wrote: > > The GenomicFeatures package in BioC 2.6 (w/ R-devel) supports the > following set of transcript tables provided by UCSC: > > track subtrack > knownGene UCSC Genes <NA> > knownGeneOld3 Old UCSC Genes <NA> > wgEncodeGencodeManualRel2 Gencode Genes Genecode Manual > wgEncodeGencodeAutoRel2 Gencode Genes Genecode Auto > wgEncodeGencodePolyaRel2 Gencode Genes Genecode PolyA > ccdsGene Consensus CDS <NA> > refGene RefSeq Genes <NA> > xenoRefGene Other RefSeq <NA> > vegaGene Vega Genes Vega Protein Genes > vegaPseudoGene Vega Genes Vega Pseudogenes > ensGene Ensembl Genes <NA> > acembly AceView Genes <NA> > sibGene SIB Genes <NA> > nscanPasaGene N-SCAN N-SCAN PASA-EST > nscanGene N-SCAN N-SCAN > sgpGene SGP Genes <NA> > geneid Geneid Genes <NA> > genscan Genscan Genes <NA> > exoniphy Exoniphy <NA> > augustusHints Augustus Augustus Hints > augustusXRA Augustus Augustus De Novo > augustusAbinitio Augustus Augustus Ab Initio > acescan ACEScan <NA> > > > Patrick > > On 3/16/10 1:18 PM, Michael Lawrence wrote: > > I think his problem is not access to UCSC but retrieving the exon > > locations. The transformation of the coordinate systems is a simple > > shift() call, once you have the exons. I don't know about > Ensembl, but > > the GenomicFeatures package provides the UCSC predictions. > > > > I just realized yesterday that all of the gene predictions stored > > within UCSC have the same, documented table format. Presumably > > rtracklayer could convert these into something like what is provided > > by GenomicFeatures, but I think GenomicFeatures already has a > function > > for doing that (building the DB). Could the utilities in > > GenomicFeatures be slightly generalized to support the alternative > > gene predictions in UCSC? > > > > Sorry for sort of hijacking the thread... > > > > Michael > > > > On Tue, Mar 16, 2010 at 11:20 AM, Patrick Aboyoun > <[email protected] <mailto:[email protected]> > > <mailto:[email protected] <mailto:[email protected]>>> wrote: > > > > Jason, > > The rtracklayer provides an interface to the UCSC browser. In > > particular rtracklayer::export can export a SimpleRleList to > a bed > > file that you can upload to UCSC. > > > > Patrick > > > > > > > > On 3/16/10 6:50 AM, Jason Lu wrote: > > > > Hi, > > > > I would like get suggestions on what is the best way to > do this. I > > have a "SimpleRleList" object, in which the range > coordinates are > > relevant to an ensembl transcript (ranges from 1 to the > total > > length > > of the transcript). I would like to show my data on the UCSC > > browser, > > so I need to map those coordinates to the genome. Currenty I > > wrote my > > own script to do this, based on the exon locations from > > biomart. There > > got to be an easy way to do this, but don't seem to find > a quick > > answer. Sorry if this has been answered. > > > > Thanks. > > > > Jason > > > > _______________________________________________ > > Bioc-sig-sequencing mailing list > > [email protected] > <mailto:[email protected]> > > <mailto:[email protected] > <mailto:[email protected]>> > > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > > > > > _______________________________________________ > > Bioc-sig-sequencing mailing list > > [email protected] > <mailto:[email protected]> > > <mailto:[email protected] > <mailto:[email protected]>> > > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > <mailto:[email protected]> > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
