Actually J, the UCSC "numbering" system isn't about bases or the gaps between bases at all, but rather intervals. For example the first base in a chromosome is the interval [0-1) The second base in a chromosome is the interval [1-2) The first and second base is the interval [0-2) And so forth. We don't apply an actual number to any specific base or gap between a base. To reference a particular nucleotide in a chromosome, the UCSC interval needs to be specified. It depends upon what label number you want to apply to that first base in the chromosome. Is it base 0 or base 1 ?
Which came first ... --Hiram ----- Original Message ----- From: "J Ireland" <[email protected]> To: "Hiram Clawson" <[email protected]> Cc: [email protected] Sent: Thursday, March 22, 2012 4:27:00 PM Subject: Re: [Genome] base vs gap numbering Hey Hiram, Nice hearing from you! OK, I don't mean to be a pain but I think I'm still not getting my question across. Let me give it one more shot, and if I'm still not making sense maybe it's a discussion to have over beers at ISMB. >From everything I've read on the UCSC site, it seems that the UCSC convention >is to number the bases themselves. As you point out, however "the hash marks >are on the "gaps" between the bases" when you zoom in. I take this to mean >you're numbering the "gaps" - not the bases. So, what's not obvious to me is >why the numbered hash marks are not over the bases (at a zoomed in level of >course) if it's the bases that are being numbered. Thanks much, -J _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
