Re: Different rendering for wiggle tracks

by Jason Stajich-3 :: Rate this Message:

Steve -

I have had the same problems - I thought some of it related to changes in the Bio::Graphics::Wiggle::Loader and how trimming was being done.

There are defaults for the trimming:

my $trim = $self->current_track->{display_options}{trim} || 'stdev2';

You can try and specify this in the your wigfile header trim=none or other combinations.

I can't remember what was the best setting to go back to the original way or if the interaction with the wiggle_xyplot changes are also the major change.

-jason

On May 28, 2009, at 8:06 AM, Steve 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
------------------------------------------------------------------
Medical Sciences Division
Weatherall Institute of Molecular Medicine/Sir William Dunn School
Oxford University

------------------------------------------------------------------------------
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
is a gathering of tech-side developers & brand creativity professionals. Meet
the minds behind Google Creative Lab, Visual Complexity, Processing, &
iPhoneDevCamp as they present alongside digital heavyweights like Barbarian
Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

Jason Stajich

jason@...

------------------------------------------------------------------------------
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
is a gathering of tech-side developers & brand creativity professionals. Meet
the minds behind Google Creative Lab, Visual Complexity, Processing, &
iPhoneDevCamp as they present alongside digital heavyweights like Barbarian
Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

« Return to Thread: Different rendering for wiggle tracks