Re: [Gmod-help] Gbrowse2 semantic feature switching

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Re: [Gmod-help] Gbrowse2 semantic feature switching

Scott Cain
Hi Noah,

I find this very strange, as it should work.  Is there anything in the
apache error_log?  Has anyone else seen similar behavior?  It appears
that the thing that most people with this problem miss (setting
"group_on = display_name") looks OK.

Scott


On Mon, Jun 7, 2010 at 10:18 PM, Noah Fahlgren
<[hidden email]> wrote:

> Hi Dave,
>
> Thanks for your help.  I attached normal and abnormal screenshots of the
> same region.  I installed Bio::Graphics 2.09 and Gbrowse 2.08.
>
> Cheers,
> Noah
>
> On 6/7/10 2:15 PM, Dave Clements, GMOD Help Desk wrote:
>
> Hi Noah,
> I can't find a problem in the configuration.  A couple of
> questions/requests:
> * What versions of GBrowse and Bio::Graphics are installed?
> * Can you send along screenshots showing both the normal and problematic
> xyplots?
> Thanks,
> Dave C.
>
> On Fri, Jun 4, 2010 at 5:04 PM, Noah Fahlgren
> <[hidden email]> 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: [hidden email]
>>
>
>
>
> --
> ===> PLEASE KEEP RESPONSES ON THE LIST <===
> http://gmod.org/wiki/GMOD_News
> http://gmod.org/wiki/Calendar
> http://gmod.org/wiki/Help_Desk_Feedback
>
>
> --
> 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: [hidden email]
>


--
------------------------------------------------------------------------
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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