Good Afternoon J: This is a perfect case to illuminate the interval notation. Note the interval this item is declared to be in [25855459-25855459) Note the size of this interval: = end - start = 25855459 - 25855459 = 0
The length of this item is ZERO ! It doesn't exist ! It can not be found in this sequence. It is somewhere between actual bases: [25855458-25855459) and [25855459-25855460) but not in this reference sequence. So, in one sense, you could say that the interval: [25855459-25855459) is actually talking about the gap between two bases. The genome browser does not show gaps at all, there are only bases and they are directly next to each other with no intervening space. We don't do gaps between bases. When you enter such a position, we can't display it, we do the next best thing and display one of the bases next to this non-existent item. I'm sure you have already seen our discussion: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms -Hiram ----- Original Message ----- From: "J Ireland" <[email protected]> To: "Hiram Clawson" <[email protected]> Cc: [email protected] Sent: Thursday, March 22, 2012 11:24:00 PM Subject: Re: [Genome] base vs gap numbering Hey Hiram, I'm definitely a firm believer in the interval, trust me - and I definitely dig the UCSC data tables and the half-open, zero-start intervals. So, rolling with the "everything is an interval" and looking up rs12345... If I zoom into the browser here: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr22%3A25855458-25855460 I see rs12345 appears to be at [25855458-25855459) given the hash marks. This is a zero-based start and end. Now, I click on rs12345 and see the position as 25855459-25855459 in the annotation page. Should I interpret this as [25855459-25855459), with a one-based start and zero-based end or as [25855459-25855459] a fully closed interval with start and end both one-based? I know you're straddling different count-starting conventions between db tables and the annotation pages. Maybe my misunderstanding is I thought the browser was using the same convention as the annotation pages, but it looks like the browser is actually more inline with the db tables... Thanks for taking this trip with me down the rabbit hole of the obscure and arcane ;) -J _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
