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 On Thu, Mar 22, 2012 at 3:23 PM, Hiram Clawson <[email protected]> wrote: > Good Afternoon J: > > If you open the browser to display a very small number of bases, say 10 > bases > from chr1:1-10 you will clearly see that it makes perfect sense. At any > other > view point beyond the base position where the bases are viewable, the hash > marks > are meaningless since there is no actual base or gap to place them on. At > any view > above base position, the hash mark itself would span several bases. > > An example 5 bases is drawn something like: > > 1| 2| 3| 4| 5| > A G C T A G > > In this case, the hash marks are on the "gaps" between the bases. > Zoom out until the bases are next to each other with no space, > there isn't any room to place hash marks and numbers. At that > point a number is mentioned only once in a while, and the hash marks > are rough guidelines: > > 5| > AGCTAG > > I'm not even sure where the hash mark is printed in that case. > All you can tell at this view point is that you are approximately 5 > bases into the sequence. Only by zooming in until the hash mark > is clearly between two bases will the actual number of the base be clear. > > --Hiram > > > J Ireland wrote: > >> 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<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<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:genome-bounces@soe.**ucsc.edu<[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<http://alternateallele.blogspot.com/2012/03/genome-coordinate-conventions.ht> >>> ml<http://alternateallele.**blogspot.com/2012/03/genome-** >>> coordinate-conventions.html<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
