[Gmod-gbrowse] Wiggle Tracks for time-series data

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[Gmod-gbrowse] Wiggle Tracks for time-series data

Peter Koppstein
We have been using GBrowse successfully with several genomes, but are currently unable to resolve two problems related to "wiggle
tracks". In brief, we are having trouble generating the kind of display show at the top of the page:
 http://gmod.org/w/index.php?title=GBrowse/Uploading_Wiggle_Tracks

We are able to display our time-series data as a single "track" consisting of a stack of multiple horizontal "wiggle plots" (one plot per time period). Furthermore, we have been able to do this both by uploading it to the backend database, and by using the "Upload your own data:" feature.

The first problem is that we have not been able to figure out how to get the stack of horizontal "wiggle" plots in the correct temporal
order when using the backend database. This problem does not arise when we use the "Upload your own data:" feature. Further details are given below.

The second problem is that, using the "Upload your own data:" feature, we haven't been able to eliminate any of the three textual lines that
appear for each horizontal plot (that is, in order, the "name", the "ref_sequence" line ("I.data"), and the "description"). Ideally we would like to present the features in the economical way shown in the figure at the top of the Uploading_Wiggle_Tracks page (i.e., with the
caption to the left of the plot).

With thanks for any pointers or hints you may be able to provide,

Peter Koppstein
Scientific Programmer
Lewis-Sigler Institute for Integrative Genomics
Princeton University

[hidden email]
w: 609 258-9104
c: 609 933-5886

GBrowse version: 1.70
Platform: Linux
Perl: 5.8.8

Ordering of the Plots within a Track
====================================

The data was uploaded to the backend database from gff3 files in which
the time is encoded as part of the "source". For example, here in
simplified form are some lines from the gff3 file representing
t=12,18,24,...:

Pf3D7_01 X_12 feature 1 10 . . . .
Pf3D7_01 X_18 feature 1 10 . . . .
Pf3D7_01 X_24 feature 1 10 . . . .
Pf3D7_01 X_30 feature 1 10 . . . .
Pf3D7_01 X_36 feature 1 10 . . . .

For the plots for time = 12, 18, ... 36, the ordering is (from top to bottom):
 24 18 12 30 36


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