Thanks for the response, Steve! Thanks for the links. I actually have seen both, but they don't quite address my question. I think you maybe misunderstood me when I refer to numbering "gaps". I don't mean "gap" as in a sequencing gaps, but rather the notion of a "space" between bases along the DNA sequence.
Anyhow, your last sentence gets to the crux of my question: "The numbering scheme in the Browser display is such that when you see a number such as 43819085 next to a hash mark, the base immediately to the left of that hash mark is base number 43819085." That's not really obvious and I'm wondering why its shown this way rather than having the hash mark over the base itself? Thanks again, -J On Thu, Mar 22, 2012 at 12:31 PM, Steve Heitner <[email protected]> wrote: > Hello, James. > > Thank you for your interest. I believe this FAQ will be helpful: > http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1. You may also want to > look at this previously-answered mailing list question: > https://lists.soe.ucsc.edu/pipermail/genome/2005-July/008162.html. > > I would also like to note that your observation that we are numbering gaps > rather than bases appears to be related to the representation of the > sequence at the top of the Browser display. As you can see from the > screenshot you provided, there is a continuous gene at that location and > thus, no gaps to number. The gaps you are referring to are merely gaps > between the letters that represent the sequence, but not gaps in the actual > sequence itself. The numbering scheme in the Browser display is such that > when you see a number such as 43819085 next to a hash mark, the base > immediately to the left of that hash mark is base number 43819085. > > Please contact us again at [email protected] if you have any further > questions. > > --- > Steve Heitner > UCSC Genome Bioinformatics Group > > -----Original Message----- > From: [email protected] [mailto:[email protected]] On > Behalf Of J Ireland > Sent: Tuesday, March 20, 2012 11:55 PM > To: [email protected] > Subject: [Genome] base vs gap numbering > > Hey cats! > > I had a question regarding base vs gap numbering on the genome browser. My > impression has been that the zero-based, half-open convention used at UCSC > was a base-numbered system. However, when you zoom in on the browser, it > appears that it's the gaps that are being numbered (as in the attached > screenshot). > > I've started collecting some thoughts on genome coordinate systems in this > draft blog post ( > > http://alternateallele.blogspot.com/2012/03/genome-coordinate-conventions.ht > ml<http://alternateallele.blogspot.com/2012/03/genome-coordinate-conventions.html> > ), > and it got me thinking/wondering about this discrepancy in my assumption > about the conventions you're using vs what I see on the browser. > > Could you set me straight? > > Thanks! > -J > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
