On Tue, Sep 1, 2009 at 10:45 AM, Jenny Qing Qian <[email protected]>wrote:
> > > On Mon, Aug 31, 2009 at 6:23 PM, Christopher Lee <[email protected]>wrote: > >> >> >> On Aug 31, 2009, at 5:57 PM, Jenny Qing Qian wrote: >> >> > For the time being, could we include an example to show how to bind >> > the ucsc gene/exon annotations to ucsc references? Has this already >> > been constructed and saved for some of the ucsc reference genomes? >> > If so, could you let us their names, so that we could access them >> > via the worldbase? >> >> No, I don't think we have such annotations plugged in. Do you know if >> the annotation data can be accessed from UCSC in a relatively simple >> way, eg. via MySQL? In that case we could probably whip up a quick >> example showing how to plug them in... > > > As the ensembl database, the ucsc database has various kinds of annotation > feature tables like exons and genes. I am not sure whether they also have a > seq_region table. I assume they directly map their annotations to their > reference genomes, not via contigs... If this is the case, then we could > just simplify the seqregion.py and work out the mapping. Agree? > There is no seqregion table. tName (PSL format) or chrom (Gene prediction, repeats) is same as chromosome name, UCSC-style like 'chr1'. And, tStart/tEnd or txStart/txEnd is the 0-based coordinates for genes (transcription units). For exons, it does not have convient way. If your exon has coordinates (10, 20), (50, 60), (100, 120), Gene prediction table (like refGene or ensGene) will save the coordinates as 10,50,100, (exonStarts field) and 20,60,120, (exonEnds). -- Namshin Kim > > >> >> >> -- Chris >> >> >> > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
