Re: [GMOD Help] GBrowse : subtrack select.

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Re: [GMOD Help] GBrowse : subtrack select.

Scott Cain
Hi Maxime,

I'm forwarding this to the GBrowse mailing list.

Scott



On Thu, Oct 17, 2013 at 10:30 AM, <[hidden email]> wrote:
Hello

On GBrowse,
Can I use subtrack select on score field in GFF3 to classify annotations regarding a threshold

exemple data
...
chrom1  test    gene    695     715     50      +       .       ID=g1;Name=G1
chrom1  test    gene    700     750     34      +       .       ID=g2;Name=G2
chrom1  test    gene    400     475     120     +       .       ID=g3;Name=G3
chrom1  test    gene    630     780     190     +       .       ID=g4;Name=G4
...

All in one track
first subtrack with G1 and G2
second subtrack with G3 and G4

something like:
subtrack select = Score ???
subtrack label = score<100; score>100;

Regards.
Maxime HEBRARD

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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: [GMOD Help] GBrowse : subtrack select.

Timothy Parnell
Hi Maxime,

I think the answer is yes and no.

Yes, you can use any standard SeqFeature method, including type, primary_tag, source, score, display_name, a named attribute, etc.

However, you must supply an exact value to match in the subtrack table to identify the tracks. So for score, you will need exact score values; you cannot provide a range to select.

For your situation, I would divide your GFF3 file into groups based on the gene score, and then add a custom GFF3 attribute to each of the genes in the groups identifying that group, and use that for the basis of the subtrack select. So group 1 will be <100, group 2 >100, etc.

Does that help?

Tim

On Oct 17, 2013, at 8:50 AM, Scott Cain <[hidden email]<mailto:[hidden email]>> wrote:

Hi Maxime,

I'm forwarding this to the GBrowse mailing list.

Scott



On Thu, Oct 17, 2013 at 10:30 AM, <[hidden email]<mailto:[hidden email]>> wrote:
Hello

On GBrowse,
Can I use subtrack select on score field in GFF3 to classify annotations regarding a threshold

exemple data
...
chrom1  test    gene    695     715     50      +       .       ID=g1;Name=G1
chrom1  test    gene    700     750     34      +       .       ID=g2;Name=G2
chrom1  test    gene    400     475     120     +       .       ID=g3;Name=G3
chrom1  test    gene    630     780     190     +       .       ID=g4;Name=G4
...

All in one track
first subtrack with G1 and G2
second subtrack with G3 and G4

something like:
subtrack select = Score ???
subtrack label = score<100; score>100;

Regards.
Maxime HEBRARD

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To view this discussion on the web visit https://groups.google.com/d/msgid/gmod-help-desk/0ab62994-c381-4a29-9837-e653f6803a2f%40googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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the latest Intel processors and coprocessors. See abstracts and register >
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------------------------------------------------------------------------------
October Webinars: Code for Performance
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Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
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