Hello Janet, Thank you for the clear examples and for including your platform and web browser info. We were able to reproduce what you are seeing, and it does indeed look like a bug. I have filed a report on it, and our engineers will be taking a look at it.
Thank you for pointing out the problem! -- Brooke Rhead UCSC Genome Bioinformatics Group On 12/8/11 4:49 PM, Janet Young wrote: > Hi there, > > I'm working with the hg18 assembly and am interested in repetitive > elements. I've found a weird behavior with the cool feature where I > can hold my mouse over a repetitive element and a little yellow box > pops up to tell me what the repeat is. Depending on the level of > zoom, sometimes the yellow box is giving me the WRONG repeat name. > This is a bit of a problem for me! Did I find a bug? I can probably > work around it by making my own version of the rmsk track with every > single element labelled with its own name, but thought maybe you'd be > interested. > > Example: This first part of my example works correctly. In this > region: chr1:15,503,628-15,509,302 (5.7kb) there is a three-part > element in the LTR track that the mouseover feature tells me > comprises THE1A - MLT-int - THE1A (the black-light gray-dark gray > thing). Those annotations match what's in the chr1.fa.out file I > downloaded a while back from your site. > > However, when I zoomed in more closely to the right-hand part of that > three-part element: chr1:15,506,240-15,506,900 now the mouse-over > tells me that the third part of the repeat (the dark gray part) is > MLT-int (when it should be THE1A). Weird. > > A second example: zoomed out = chr2:108,069,237-108,076,256, > zoomed in = chr2:108,072,403-108,073,328 (again the right-hand part > of a three-part repeat gets wrong annotation. > > And a third, same kind of thing: zoomed out = > chr12:7,577,008-7,581,757 zoomed in= chr12:7,578,795-7,579,676 (and > I have more examples but that's probably enough!) > > Does this make any sense to you? I'm curious whether it's > reproducible. Let me know if you need more explanation. > > I'm working on a Mac, and see the same problem on both Safari and > Firefox. > > thanks, and best wishes, > > Janet Young > > > > ------------------------------------------------------------------- > > Dr. Janet Young > > Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., > C3-168, P.O. Box 19024, Seattle, WA 98109-1024, USA. > > tel: (206) 667 1471 fax: (206) 667 6524 email: jayoung ...at... > fhcrc.org > > > ------------------------------------------------------------------- > > > > > _______________________________________________ Genome maillist - > [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
