Turn some Wiggle tracks off when no value in selected region

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Turn some Wiggle tracks off when no value in selected region

Kai Xia

I am using wiggle format (Gbrowse 1.x) to display eQTL results. there are 20
000 tracks in total. By default Gbrowse just shows all the track even though
there is no value for most of the tracks in a selected genomic region. So my
question is:
Is it a configuration to customize the display and let the Gbrowse only
shows the tracks having values in the selected genomic region. I have to use
wiggle format because the data file is too big to use gff3 format.

Kai Xia
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callback on glyphs

DDI (FH) Andreas Redl
I was wondering if it is possible to use callbacks for glyphs too. There is
a workaround that will do it (2 tracks instead of one) but I am curious and
would use the callback option rather. Many thanks!

Andreas Redl



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Re: Turn some Wiggle tracks off when no value in selected region

Lincoln Stein
In reply to this post by Kai Xia
Hi Kai,

You have 20,000 (2e4) tracks?! I'm surprised that GBrowse works at all under those conditions. Do these all tracks have separate configurations or are you lumping the wiggle data into the same track?

In GBrowse 2, there is a way to group wiggle files together to create subtracks. Currently the subtracks display even if there is no data displaying in the region, but I can make this configurable.

Lincoln

On Tue, Jul 6, 2010 at 12:27 PM, Kai Xia <[hidden email]> wrote:

I am using wiggle format (Gbrowse 1.x) to display eQTL results. there are 20
000 tracks in total. By default Gbrowse just shows all the track even though
there is no value for most of the tracks in a selected genomic region. So my
question is:
Is it a configuration to customize the display and let the Gbrowse only
shows the tracks having values in the selected genomic region. I have to use
wiggle format because the data file is too big to use gff3 format.

Kai Xia
--
View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/Turn-some-Wiggle-tracks-off-when-no-value-in-selected-region-tp943355p943355.html
Sent from the gmod-gbrowse mailing list archive at Nabble.com.

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Re: callback on glyphs

Lincoln Stein
In reply to this post by DDI (FH) Andreas Redl
This sort of thing works:

   glyph        = sub { my $strand = shift->strand; return $strand >=0 ? 'gene' : 'box' }

Lincoln

On Tue, Jul 6, 2010 at 12:45 PM, DDI (FH) Andreas Redl <[hidden email]> wrote:
I was wondering if it is possible to use callbacks for glyphs too. There is
a workaround that will do it (2 tracks instead of one) but I am curious and
would use the callback option rather. Many thanks!

Andreas Redl



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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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Re: callback on glyphs

Keiran Raine
In reply to this post by DDI (FH) Andreas Redl
Hi,

Depending on the source of your data you can use a callback for pretty much any of the configurable components of a track.

The exception is tracks generated as 'remote feature's. I think the only restrictions would be using compatible glyphs such as triangle (different orientations can be set), cross and generic should all work together.

I can send some examples if useful to anyone.

Regards, Keiran

Sent from my Android phone

-----Original Message-----
From: DDI \(FH\) Andreas Redl [[hidden email]]
Received: 06/07/2010 18:08
To: [hidden email] [[hidden email]]
Subject: [Gmod-gbrowse] callback on glyphs



I was wondering if it is possible to use callbacks for glyphs too. There is
a workaround that will do it (2 tracks instead of one) but I am curious and
would use the callback option rather. Many thanks!

Andreas Redl



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Re: Turn some Wiggle tracks off when no value in selected region

Kai Xia
In reply to this post by Lincoln Stein

Hi Lincoln,
Actually I haven't tried 20, 000 tracks yet. I did tried 100 tracks and
found out all the tracks are displayed even though there were no data. If
possible lumping the wiggle data into the same track will also be great for
me as long as there is legend for each line.
So you mean only Gbrowse 2 can do this? Could you tell me how and is this
version stable right now for website use?
Thank you so much.
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Re: Turn some Wiggle tracks off when no value in selected region

Lincoln Stein
Hi Kai,

I think you'll find that 20,000 track definitions are going to slow GBrowse down to the point of unusability. I have made some fixes to GBrowse2 that allow you to display > 1000 tracks with reasonable performance, but I've never tested in the 10,000 track range.

If you combine wiggle data into subtracks, then performance in GBrowse2 should be quite good. There is also an interface that lets you define metadata for each subtrack and search, filter and sort on the basis of this metadata (see http://gmod.org/wiki/Creating_and_Managing_Subtracks_with_GBrowse2). I've also just now added an option that lets you hide subtracks that have no data currently showing.

My opinion is that GBrowse2 is ready for production use and encourage you to take a look.

Lincoln

On Tue, Jul 6, 2010 at 4:49 PM, Kai Xia <[hidden email]> wrote:

Hi Lincoln,
Actually I haven't tried 20, 000 tracks yet. I did tried 100 tracks and
found out all the tracks are displayed even though there were no data. If
possible lumping the wiggle data into the same track will also be great for
me as long as there is legend for each line.
So you mean only Gbrowse 2 can do this? Could you tell me how and is this
version stable right now for website use?
Thank you so much.
--
View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/Turn-some-Wiggle-tracks-off-when-no-value-in-selected-region-tp943355p946349.html
Sent from the gmod-gbrowse mailing list archive at Nabble.com.

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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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Re: Turn some Wiggle tracks off when no value in selected region

Kai Xia

Thank you so much Lincoln
Your solutions looks very promising.
I will tried to use Gbrowse2.
Many thanks
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