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
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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
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