[Gmod-help] Re: [Gmod-gbrowse] [GBrowse2] NGS Coverage detail

[Scott Cain]

Hi Andreas,

I think Lincoln is working on a semantic zooming bug, so this may be
related to that.

Scott


On Thu, Feb 4, 2010 at 10:27 AM, Andreas Kuntzagk
<andreas.kuntzagk at mdc-berlin.de> wrote:
> Dear Scott,
>
> unfortunately this does not work when set for a zoom level. I want to
> display coverage when detail is bigger than 10kbp and the actual read
> otherwise. This is my track definition:
>
> ====
> #NGS tracks
> [read_tophat_s4]
> feature        = read_pair
> glyph          = segments
> #link           =
> draw_target    = 1
> show_mismatch  = 1
> mismatch_color = red
> database       = tophat_s4
> bgcolor       = sub {
>                my $f = shift;
>                return $f->attributes('M_UNMAPPED') ? 'red' : 'green';
>                }
> fgcolor       = green
> height         = 3
> label density  = 50
> bump           = fast
> connector     = dashed
> balloon hover = sub {
>                my $f     = shift;
>                return '' unless $f->type eq 'match';
>                return 'Read: '.$f->display_name.' : '.$f->flag_str;
>                }
>
> key            = Read pairs s4 tophat mapped
> category       = Solexa
>
> [read_tophat_s4:9999]
> feature     = coverage
> glyph       = wiggle_xyplot
> database    = tophat_s4
> link        =
>
> ====
>
> This disables the link completely for the track. If I take out the first
> "link =  " line, it will be enabled even when zoomed out and displaying
> coverage.
>
> regards, Andreas
>
> Scott Cain wrote:
>>
>> Hi Andreas,
>>
>> That certainly feels like a bug that needs fixing.  If you want to
>> turn hyperlinks off for a track, you can set
>>
>>  link =
>>
>> That is, with nothing after the equals sign.
>>
>> Scott
>>
>>
>> On Wed, Feb 3, 2010 at 4:13 AM, Andreas Kuntzagk
>> <andreas.kuntzagk at mdc-berlin.de> wrote:
>>>
>>> Hi,
>>>
>>> It's still not working. Since I have no idea what to display I could live
>>> with this link disabled. Unfortunately I've not figured out how to
>>> disable
>>> it. (Default for all tracks is AUTO)
>>>
>>> regards, Andreas
>>>
>>> Dave Clements, GMOD Help Desk wrote:
>>>>
>>>> Hi Andreas.
>>>>
>>>> I admit that I never gave any thought to what GBrowse should display
>>>> when you click on a SAM/BAM based coverage plot.
>>>>
>>>> Is this still not working for you?  I'm hoping (but doubtful) that the
>>>> patch to GBrowse_details in another one of your email threads
>>>> ("gbrowse_detail not working anymore") fixed this problem.
>>>>
>>>> Thanks,
>>>>
>>>> Dave C.
>>>>
>>>> On Wed, Jan 27, 2010 at 6:48 AM, Andreas Kuntzagk
>>>> <andreas.kuntzagk at mdc-berlin.de> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> I followed the GBrowse NGS tutorial to add some solexa data to our
>>>>> GBrowse installation. I have a nice coverage plot. But when I click on
>>>>> it, I get an error page:
>>>>>
>>>>> Requested feature not found in database.
>>>>>
>>>>> The error log shows:
>>>>> search_features(-search_term=>coverage:1000:v31.001111 coverage):
>>>>> cannot
>>>>> calculate coverage unless a -seq_id is provided at
>>>>> /usr/local/lib/perl/5.8.8/Bio/Graphics/Browser2/Region.pm line 306
>>>>>
>>>>> What is supposed to be displayed as detail page for the coverage plot
>>>>> and where can I search for the error cause?
>>>>> Or how do I disable the link?
>>>>>
>>>>> regards, Andreas
>>>>>
>>>>>
>>>>>
>>>>>
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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