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

[Jason Stajich]

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~
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>> _______________________________________________
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>> Gmod-gbrowse at lists.sourceforge.net
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>>
>>
>
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