Re: Different rendering for wiggle tracks

by Lincoln Stein-3 :: Rate this Message:

Hi Steve,

The wiggle code was recently moved out of GBrowse and into a separate Bio::Graphics distribution. At the same time we removed the default smoothing to better render the raw data. Could you try to download the CPAN version of Bio::Graphics and install it on top of the GBrowse-CVS version? If the data continues to look wrong, I will fix it.

Lincoln

On Thu, May 28, 2009 at 11:06 AM, Steve Taylor <stephen.taylor@...> wrote:

Hi,

We have two installations of gbrowse for our production and test environment.

(1) The gbrowse production server was from the 1.69 tar ball using ActivePerl-5.8.8.822, and run with bioperl-live as on 2008-09-04
(2) On the gbrowse development server we installed GBrowse-CVS as on 2009-03-19 using netinstall to see if this would fix some problems

However, on (2) we noticed there is a difference in the way wiggle tracks are rendering. The (2) version looks smoothed and wrong compared with the raw data.
Was this type of rendering desired? We notice the wiggle_xyplot.pm code is completely different.

To see what I mean have a look at:

(1) http://sara.molbiol.ox.ac.uk/userweb/staylor/gbrowse/gbrowse.jpg
(2) http://sara.molbiol.ox.ac.uk/userweb/staylor/gbrowse/gbrowsedev.jpg

The age old question :-) do we wait for 1.7 to fix this or is this type of rendering likely to stay?

Kind regards and thanks,

Steve
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