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

Fri Apr 30 15:36:15 EDT 2010

Yes, except I need to display both strands for the EST glyph. I also need to show mismatch based on more than one reference sequence.
On Apr 30, 2010, at 11:44 AM, Scott Cain wrote:

> 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
>>>>>>> 
>>>>>>> 
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> 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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>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>> 
>>>> 
>>> 
>>> 
>>> 
>>> --
>>> ------------------------------------------------------------------------
>>> 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