Discussion:
[Gmod-gbrowse] FFF multiple sequence ID issue
Vladimir Gritsenko
2015-02-25 16:28:33 UTC
Permalink
Hello all,

I’m having a problem with an FFF file. It defines an xyplot histogram, and includes multiple sequence IDs. However, GBrowse 2.49 (as deployed on CGD) files all features under the first sequence ID it encounters, and ignored the rest.

This leads to me another question. Is there a “canonical" version of GBrowse against which potential bugs can be tested?

The test data is:

[CNV]
glyph = xyplot
graph_type=histogram
fgcolor = black
bgcolor = black
height=50
min_score=0
max_score=4
label=1
key=CNV histogram

CNV " " Ca21chr1_C_albicans_SC5314:1..5000 score=4

CNV " " Ca21chr2_C_albicans_SC5314:1..5000 score=3
Vladimir Gritsenko
2015-03-01 14:39:20 UTC
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In case anyone else runs into this, my solution was to switch to GFF3. One potential issue to resolve is aggregation - every data point will be its own plot, flooding the track with axes. The solution is to aggregate all the desired data points under the same ID, so it looks something like this:

Ca22chrRA_C_albicans_SC5314 Ymap CNV 81 100 2.5 . . ID=C1
Ca22chrRA_C_albicans_SC5314 Ymap CNV 101 120 2.5 . . ID=C1

Ca22chr1A_C_albicans_SC5314 Ymap CNV 20 40 2 . . ID=C2
Ca22chr1A_C_albicans_SC5314 Ymap CNV 41 60 1 . . ID=C2
Post by Vladimir Gritsenko
Hello all,
I’m having a problem with an FFF file. It defines an xyplot histogram, and includes multiple sequence IDs. However, GBrowse 2.49 (as deployed on CGD) files all features under the first sequence ID it encounters, and ignored the rest.
This leads to me another question. Is there a “canonical" version of GBrowse against which potential bugs can be tested?
[CNV]
glyph = xyplot
graph_type=histogram
fgcolor = black
bgcolor = black
height=50
min_score=0
max_score=4
label=1
key=CNV histogram
CNV " " Ca21chr1_C_albicans_SC5314:1..5000 score=4
CNV " " Ca21chr2_C_albicans_SC5314:1..5000 score=3
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