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

[Andreas Kuntzagk]

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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>>>
>>>
>>
> 
> 
>