[Gmod-help] Gbrowse2 semantic feature switching

[Lincoln Stein]

Hi Noah,

Please confirm: the histogram is working correctly when you make it the
primary stanza instead of the semantically zoomed stanza? I think I know
what the problem is. If you can, please try patching
Bio/Graphics/Browser2/RenderPanels.pm with the enclosed patch file. I am 90%
sure it will fix the problem.

Lincoln

On Fri, Jun 4, 2010 at 8:04 PM, Noah Fahlgren <fahlgren at cgrb.oregonstate.edu
> wrote:

> I have a database populated with sequenced small RNA and I am trying to
> create a track that displays the individual sequences below 1,000 nts and
> displays histogram density data with scrolling windows above.  Here is my
> track configuration:
>
> [lib127]
> feature         = smallRNA127
> database        = smallRNA
> glyph           = generic
> key             = Col-0
> height          = 4
> fgcolor         = \&multicolorDisplay
> bgcolor         = \&multicolorDisplay
> strand_arrow    = 1
> description     = 0
> label           = sub {
>                        my $feature = shift;
>                        my $note = $feature->score." RPM";
>                        return $note;
>                }
> label_density   = 50
> bump density    = 1000
> category        = Fahlgren et al. 2009
> citation        = small RNA from wild type (Col-0) whole-aerial, bolting
> plants (Fahlgren et al. 2009).
>
> [lib127:1000]
> feature         = smallRNA127_100
> database        = histograms
> glyph           = xyplot
> height          = 50
> fgcolor         = black
> bgcolor         = black
> strand_arrow    = 0
> description     = 0
> label           = 0
> group_on        = display_name
> graph_type      = boxes
> max_score       = 100
> min_score       = -100
> clip            = 1
> part_color      = \&multicolorDisplay
>
> When I zoom out to 1,000 nts or more I get individual xyplot graphs for
> each datapoint instead of a continuous graph. If I make the xyplot stanza
> the default feature then I get normal xyplots. Here is a sample of what I
> loaded into our Bio::DB::SeqFeature MySQL database:
>
> Individual small RNA:
> Chr1    ASRP    smallRNA127    75    98    1.52    -    .
>  ID=ASRP1672607;Index=0
> Chr1    ASRP    smallRNA127    154    177    1.52    +    .
>  ID=ASRP782716;Index=0
> Chr1    ASRP    smallRNA127    170    192    4.56    +    .
>  ID=ASRP331607;Index=0
> Chr1    ASRP    smallRNA127    171    194    1.52    +    .
>  ID=ASRP7739156;Index=0
> Chr1    ASRP    smallRNA127    543    566    1.52    +    .
>  ID=ASRP2341059;Index=0
> Chr1    ASRP    smallRNA127    594    617    1.52    +    .
>  ID=ASRP3944461;Index=0
> Chr1    ASRP    smallRNA127    752    775    1.52    +    .
>  ID=ASRP2891574;Index=0
> Chr1    ASRP    smallRNA127    772    795    1.52    +    .
>  ID=ASRP827103;Index=0
>
> Histogram data:
> Chr1    ASRP    smallRNA127_100    110    130    1.52    +    .
>  Name=smallRNA127_100;SizeClass=24;Index=0
> Chr1    ASRP    smallRNA127_100    130    150    7.6    +    .
>  Name=smallRNA127_100;SizeClass=23;Index=0
> Chr1    ASRP    smallRNA127_100    150    170    7.6    +    .
>  Name=smallRNA127_100;SizeClass=23;Index=0
> Chr1    ASRP    smallRNA127_100    170    190    7.6    +    .
>  Name=smallRNA127_100;SizeClass=23;Index=0
> Chr1    ASRP    smallRNA127_100    190    210    7.6    +    .
>  Name=smallRNA127_100;SizeClass=23;Index=0
> Chr1    ASRP    smallRNA127_100    210    230    6.08    +    .
>  Name=smallRNA127_100;SizeClass=23;Index=0
> Chr1    ASRP    smallRNA127_100    510    530    1.52    +    .
>  Name=smallRNA127_100;SizeClass=24;Index=0
> Chr1    ASRP    smallRNA127_100    530    550    1.52    +    .
>  Name=smallRNA127_100;SizeClass=24;Index=0
> Chr1    ASRP    smallRNA127_100    550    570    3.04    +    .
>  Name=smallRNA127_100;SizeClass=24;Index=0
>
> Am I missing something?  I used to do this in Gbrowse 1.7, but maybe
> something has changed.
>
> Thanks,
> Noah
>
> --
> Noah Fahlgren
> Graduate Research Assistant
> Center for Genome Research and Biocomputing
> 3021 ALS Building
> Oregon State University
> Corvallis, OR 97331
> Phone: 541-737-3679
> Email: fahlgren at cgrb.oregonstate.edu
>
>


-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
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