[Gmod-help] Re: [Gmod-gbrowse] features do not line up.

[Scott Cain]

This one is weird because the 'group_pattern' option should also make
them line up vertically, but it doesn't seem to be doing that.  It's
not clear to me why.  Jeff, could you send me a sample of data that
reproduces this problem (preferable a fairly small sample :-)

Thanks,
Scott


On Wed, Jul 30, 2008 at 4:18 PM, Jason Stajich <jason at bioperl.org> wrote:
> did you try playing with the bumping level. That might help?
> -jason
> On Jul 30, 2008, at 1:15 PM, Dave Clements, GMOD Help Desk wrote:
>
>> Jeff,
>>
>> Have you had any luck finding a workaround for this problem?  If you
>> have, can you post a short description to this list?  If you haven't,
>> please post that as well, and I'll investigate.
>>
>> Apologies for the delayed response.  Many of us have been on the road
>> for most of July.
>>
>> Thanks,
>> Dave C
>> GMOD Help Desk
>>
>> On Mon, Jul 14, 2008 at 1:33 PM, Jeff Chu <jeff.sc.chu at gmail.com>
>> wrote:
>>> Hi All,
>>> I'm having trouble getting a proper image on a gbrowse that I'm
>>> setting up.
>>> I am uploading paired end reads from Solexa sequencing. Each read is
>>> represented by a green box. The paired reads are connected by a
>>> dotted line.
>>> However, for many paired reads, the boxes do not line up on the same
>>> horizontal plane.
>>> I'm wondering is there any things to change in the .conf file to
>>> fix this.
>>> I've attached an image to illustrate the problem.
>>>
>>> Below is the track configuration in the conf file.
>>>
>>> [SOLEXA_CE0131]
>>> feature      = alignment:solexaCE0131
>>> glyph        = segments
>>> category     = SOLEXA
>>> height       = 6
>>> draw_target   = 1
>>> show_mismatch = 1
>>> canonical_strand = 1
>>> group_pattern   =       /_[12]$/
>>> bgcolor      = limegreen
>>> label   =       sub{
>>>         my $feature = shift;
>>>         my $name = $feature->name;
>>>         $name =~ s/solexaCE0131_//;
>>>         return $name;
>>>         }
>>> key          = Solexa reads daf-19;daf-12
>>>
>>> --
>>> rejoice,
>>> jeff~
>>> ---------------------------------------------------------------------
>>> ----
>>> Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW!
>>> Studies have shown that voting for your favorite open source project,
>>> along with a healthy diet, reduces your potential for chronic
>>> lameness
>>> and boredom. Vote Now at http://www.sourceforge.net/community/cca08
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> Gmod-gbrowse at lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>
>>>
>>
>> --
>> Was this helpful? Let us know at http://gmod.org/Help_Desk_Feedback
>>
>> ----------------------------------------------------------------------
>> ---
>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>> challenge
>> Build the coolest Linux based applications with Moblin SDK & win
>> great prizes
>> Grand prize is a trip for two to an Open Source event anywhere in
>> the world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D. cain.cshl at gmail.com
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory