I'll take a look. Thanks for taking the effort to make the test files.


On Tue, Mar 22, 2011 at 1:44 AM, Timothy Parnell <Timothy.Parnell@hci.utah.edu> wrote:
Just as a followup, I'm including some sample files which should load into
the example Yeast database provided with GBrowse. If you have
Bio::DB::BigFile installed, you should be able to load these files using
the Custom Tracks upload file function. You can confirm the track000.bw
file is generated in the appropriate userdata temp folder. (I have not
tried these in GBrowse without BigFile support installed).

File chrI_sparse is a variableStep wig file with 25 random data points
across chrI.

File chrI_step10 is essentially the same data as fixedStep in 10 bp steps,
with 0 recorded at intervening positions.

Playing with these samples, I've noticed a couple of "rules".

Loading 20 Kb from chrI:141,500..161,499 yields rendered tracks for both.
Zooming in to 5 kb and the chrI_sparse cannot render (only one datapoint
available), while chrI_step10 can (500 datapoints with one non-zero).

Loading any region with two or more datapoints seems to be fine for either

Loading a region with zero datapoints results in an opposite effect. Go to
chrI:161,850..211,849 with a 50 kb region. Both tracks are rendered fine.
Zoom in to 5 kb, where there are no datapoints. Now chrI_sparse correctly
renders an empty track (no datapoints) but chrI_step10 fails to render
(500 datapoints, all zero).

I admit these situations may be relatively rare, but not contrived.

On 3/21/11 11:48 AM, "Timothy Parnell" <Timothy.Parnell@hci.utah.edu>

>I have a lab mate who is trying to visualize her genomic data with a
>bigwig file. The data happens to be pretty sparse, for example, maybe a
>dozen positions or less with a recorded value in a 10 kb window. These
>tend to fail to render. If you zoom out to 50 or 100 kb, then the track
>renders properly, presumably because there are now enough data points? If
>there are no data points in the requested region, then we get an empty
>track, as expected (no scale bars, only vertical grid lines).
>So far, this seems to happen regardless whether the source file was a
>variableStep wig or bedGraph file.
>I hadn't seen this before, but then all my data was fixedStep. I
>converted her sparse data to a fixedStep wig (assigning 0 to the empty
>positions, of course), and the track renders beautifully as expected,
>regardless of zoom level.
>Is this a bug, or an unintentional side effect of the data formatting?
>Has anyone else seen this phenomenon?
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>A question and answer guide to determining the best fit
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