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

[Artemus Harper]

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
>>>
>>>
>>> ------------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> 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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