[Gmod-help] Re: [Gmod-gbrowse] Glyph 'dna' display problem

[Scott Cain]

Hi Artemus,

I'm not sure I understand: the dna glyph is only really usable for the
reference sequence (ie, the chromosome or whatever the other features
a drawn in reference to).  Other glyphs like generic and segments know
how to draw dna when zoomed in.  Is that what you want?

Scott


On Fri, Apr 30, 2010 at 2:09 PM, Artemus Harper <subanark at gmail.com> wrote:
> Ok, I updated to the newest version of gbowse (the new version is at:
> http://vm-gmod.eecs.wsu.edu/cgi-bin/gb2/gbrowse/primer2/?start=253;stop=352;ref=genome;width=800;version=100;flip=0;grid=1;id=1ae82ac1261f191c48bd51641c91191a;label=DNA-Primer)
>
> As you can see I am still seeing the same glyph problem.
>
> On Mon, Apr 26, 2010 at 1:45 PM, Artemus Harper <subanark at gmail.com> wrote:
>>
>> I do have an old version of Gbrowse (not sure how to determine my current
>> version), I'm trying to update it right now, but I'm running into some
>> issues. The install script says it cannot find CBuilder.pm, which I assume
>> may be included in a newer version of perl I have installed (5.8.8) which
>> according to the wiki is high enough to install with. I'll get perl updated
>> once I resolve my conflict with the repos.
>>
>> On Mon, Apr 26, 2010 at 12:49 PM, Dave Clements, GMOD Help Desk
>> <help at gmod.org> wrote:
>>>
>>> Hi Artemus,
>>> I think you've found a bug.  The primers appear to only be correctly
>>> aligned when the view includes the start point for the primer.  The code is
>>> also showing too much DNA for the primers, making the primer DNA image be
>>> too wide.
>>> Does anyone have an idea on this, other than a coding bug?
>>> Thanks,
>>> Dave C.
>>>
>>>
>>> On Fri, Apr 23, 2010 at 11:09 AM, Artemus Harper <subanark at gmail.com>
>>> wrote:
>>>>
>>>> I'm trying to use the glyph dna to see nucleotide sequences when you
>>>> zoom in. However, this doesn't seem to be working for features. In
>>>> particular, if a contig refers to a part of another contig, it isn't
>>>> displaying the right data when the start of the sequence is not in view.
>>>>
>>>> For example, I'm looking at one of my sequences starting at
>>>> genome:470.570. I see:
>>>>
>>>> <-----------------------------------------------
>>>> 470
>>>> DNA/GC Content
>>>> tgtgatttctatgttatgta...
>>>>
>>>> Primers
>>>>    S4
>>>>    gatttctatgttatgta...
>>>>
>>>> But when I move over to the right:
>>>> <-----------------------------------------------
>>>> 500
>>>> DNA/GC Content
>>>> taagggcatatcggttgaag...
>>>>
>>>> Primers
>>>> S4
>>>>  cgaagaaacaaattatattt...
>>>>
>>>> which for S4 isn't what was displayed at 500, although it is for the
>>>> genome sequence.
>>>>
>>>> You can see this yourself (when the two tracks are turned on):
>>>> http://gmod.eecs.wsu.edu/cgi-bin/gbrowse/primer2/?name=genome:470..570
>>>> and when shifted over:
>>>> http://gmod.eecs.wsu.edu/cgi-bin/gbrowse/primer2/?name=genome:500..600
>>>> --
>>>> Artemus Harper
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>>
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>>>> Gmod-gbrowse at lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>
>>>
>>>
>>>
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>>
>>
>>
>> --
>> Artemus Harper
>
>
>
> --
> Artemus Harper
>
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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