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

[Scott Cain]

Hi Artemus,

Do you want to do something like figure 18 in the tutorial:

  http://gmod.org/gbrowse-cgi/tutorial/tutorial.html#multiple_alignments

Scott


On Fri, Apr 30, 2010 at 2:33 PM, Artemus Harper <subanark at gmail.com> wrote:
> I am looking for a way to show primers at the nucleotide level with the enhancers marked as such and any part that doesn't match all the reference sequences highlighted (this also means I need to show multiple reference sequences, although I can probably hide the true reference sequence).
> On Apr 30, 2010, at 11:18 AM, Scott Cain wrote:
>
>> 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 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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>>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>



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