[Gmod-help] Re: [Gmod-gbrowse] wiggle_xyplot smoothing

[Timothy Parnell]

Hi Dave,
Yes, I forgot to mention this in my first email. I'm using the latest relevant distributions available from CPAN.

GBrowse-2.08
Bio-Graphics-2.09
BioPerl-1.6.1

I have not tried checking anything out from the live developer versions. Should I try those?

Tim

On 5/25/10 3:54 PM, "Dave Clements, GMOD Help Desk" <help at gmod.org> wrote:

Hi Timothy,

I'm pretty sure this is a a bug.  I know the wig rendering code has been touched in the last year or so.  What version of GBrowse is this happening in?  I'm hopeful that upgrading will solve this problem.

Dave C.

On Mon, May 24, 2010 at 9:02 AM, Timothy Parnell <Timothy.Parnell at hci.utah.edu> wrote:
Hello,

I'm having issues with the smoothing of wiggle data when rendering a track in GBrowse. Specifically, turning smoothing off.

I have the same high resolution microarray data loaded both into a SeqFeature::Store database as well as binary wiggle files (via the wiggle2gff3.pl <http://wiggle2gff3.pl>  script). Viewing tracks from each data source gives vastly different graphs (see attached image). It's most apparent with the histogram plot. It appears that the wiggle track is automatically binning the data to smooth it. However, I anticipate the "noisy" data as seen in the database track, and it would be nice to see it in the wiggle track.

I have set the smoothing option to "none" in the wiggle track configuration, but GBrowse appears to be ignoring this line. The smoothing occurs at zoom levels above 2 kb, whereas at 1 kb or below the tracks are the same. I can pull the data back out of the database and wiggle files (using either custom scripts or downloading track data from GBrowse) and the data is identical (within expectations of converting the data to 8-bit dynamic range).

Is there a way to control the semantic automatic smoothing of wiggle data? Is my configuration set incorrectly? Or is this a bug?

My track conf is below:

[sample_chip_wig1]
feature      = deg_con_ratio_mono1_wig
glyph        = wiggle_xyplot
graph_type   = histogram
height       = 50
scale        = left
label        = 0
autoscale    = global
bicolor_pivot = zero
pos_color    = blue
neg_color    = red
smoothing    = none
smoothing_window = 1
key          = sample_chip_wig1

[sample_chip_db1]
feature      = deg_con_ratio_mono1_244k
glyph        = xyplot
graph_type   = histogram
height       = 50
scale        = left
fgcolor      = black
min_score    = -2
max_score    = 2
label        = 0
group_on     = display_name
key          = sample_chip_db1

Thanks for any assistance

--

Timothy J Parnell, PhD.
Research Associate
Howard Hughes Medical Institute
Department of Oncology
Huntsman Cancer Institute
University of Utah
Salt Lake City, UT 84112


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