[Gmod-ajax] Are tabix indexed BED files supported?

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[Gmod-ajax] Are tabix indexed BED files supported?

Keiran Raine
Hi,

I'm looking to plot lines and points (coverage segmentation data) within JBrowse.  It seems that a tabix indexed BED file would be appropriate to do this as it supports single and range based segments as well as a score value to indicate the vertical position of the value.

As VCF is tabix indexed is this something that could be easily added.

I'm looking for something relatively simple like the following (but most likely within the same track):




Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104


-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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Re: Are tabix indexed BED files supported?

Robert Buels-2
It would be relatively easy to add, but I could use some help.

Any chance you'd want to take a crack at it?


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 11/29/2013 01:49 PM, Keiran Raine wrote:

> Hi,
>
> I'm looking to plot lines and points (coverage segmentation data) within
> JBrowse.  It seems that a tabix indexed BED file would be appropriate to
> do this as it supports single and range based segments as well as a
> score value to indicate the vertical position of the value.
>
> As VCF is tabix indexed is this something that could be easily added.
>
> I'm looking for something relatively simple like the following (but most
> likely within the same track):
>
>
>
>
> Keiran Raine
> Principal Bioinformatician
> Cancer Genome Project
> Wellcome Trust Sanger Institute
>
> [hidden email] <mailto:[hidden email]>
> Tel:+44 (0)1223 834244 Ext: 7703
> Office: H104
>
>
> -- The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.
>
>
> ------------------------------------------------------------------------------
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
> http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

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Re: Are tabix indexed BED files supported?

Keiran Raine
If you can point me to the relevant bits of code to look at I'll have a go (gulping as I type)

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 2 Dec 2013, at 16:04, Robert Buels <[hidden email]> wrote:

It would be relatively easy to add, but I could use some help.

Any chance you'd want to take a crack at it?


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 11/29/2013 01:49 PM, Keiran Raine wrote:
Hi,

I'm looking to plot lines and points (coverage segmentation data) within
JBrowse.  It seems that a tabix indexed BED file would be appropriate to
do this as it supports single and range based segments as well as a
score value to indicate the vertical position of the value.

As VCF is tabix indexed is this something that could be easily added.

I'm looking for something relatively simple like the following (but most
likely within the same track):




Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

[hidden email] <[hidden email]>
Tel:+44 (0)1223 834244 Ext: 7703
Office: H104


-- The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.


------------------------------------------------------------------------------
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk



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-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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Re: Are tabix indexed BED files supported?

Robert Buels-2
Well, you'd probably want to make a
src/JBrowse/Store/SeqFeature/BEDTabix.js file, which would look a lot
like the VCFTabix.js file in the same directory, but you probably
wouldn't need to do the VCFIndexedFile subclass of TabixIndexedFile, and
you would need to also implement a lineToFeature method instead of
inheriting from a separate VCFParser class like that one does.

I'm in the #gmod IRC channel on freenode during business hours US East,
always happy to give live help.

Is that enough to get you started?


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org


On 12/02/2013 11:10 AM, Keiran Raine wrote:

> If you can point me to the relevant bits of code to look at I'll have a
> go (gulping as I type)
>
> Keiran Raine
> Principal Bioinformatician
> Cancer Genome Project
> Wellcome Trust Sanger Institute
>
> [hidden email] <mailto:[hidden email]>
> Tel:+44 (0)1223 834244 Ext: 7703
> Office: H104
>
> On 2 Dec 2013, at 16:04, Robert Buels <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>> It would be relatively easy to add, but I could use some help.
>>
>> Any chance you'd want to take a crack at it?
>>
>>
>> Robert Buels
>> Lead Developer
>> JBrowse - http://jbrowse.org
>>
>> On 11/29/2013 01:49 PM, Keiran Raine wrote:
>>> Hi,
>>>
>>> I'm looking to plot lines and points (coverage segmentation data) within
>>> JBrowse.  It seems that a tabix indexed BED file would be appropriate to
>>> do this as it supports single and range based segments as well as a
>>> score value to indicate the vertical position of the value.
>>>
>>> As VCF is tabix indexed is this something that could be easily added.
>>>
>>> I'm looking for something relatively simple like the following (but most
>>> likely within the same track):
>>>
>>>
>>>
>>>
>>> Keiran Raine
>>> Principal Bioinformatician
>>> Cancer Genome Project
>>> Wellcome Trust Sanger Institute
>>>
>>> [hidden email] <mailto:[hidden email]> <mailto:[hidden email]>
>>> Tel:+44 (0)1223 834244 Ext: 7703
>>> Office: H104
>>>
>>>
>>> -- The Wellcome Trust Sanger Institute is operated by Genome Research
>>> Limited, a charity registered in England with number 1021457 and a
>>> company registered in England with number 2742969, whose registered
>>> office is 215 Euston Road, London, NW1 2BE.
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Rapidly troubleshoot problems before they affect your business. Most IT
>>> organizations don't have a clear picture of how application performance
>>> affects their revenue. With AppDynamics, you get 100% visibility into
>>> your
>>> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of
>>> AppDynamics Pro!
>>> http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk
>>>
>>>
>>>
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>
>
> -- The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
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Re: Are tabix indexed BED files supported?

Keiran Raine
Hi Robert,

That's great, I'll keep you informed, probably going to be doing this mostly in my own time so mat be a little while...

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 2 Dec 2013, at 16:26, Robert Buels <[hidden email]> wrote:

Well, you'd probably want to make a src/JBrowse/Store/SeqFeature/BEDTabix.js file, which would look a lot like the VCFTabix.js file in the same directory, but you probably wouldn't need to do the VCFIndexedFile subclass of TabixIndexedFile, and you would need to also implement a lineToFeature method instead of inheriting from a separate VCFParser class like that one does.

I'm in the #gmod IRC channel on freenode during business hours US East, always happy to give live help.

Is that enough to get you started?


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org


On 12/02/2013 11:10 AM, Keiran Raine wrote:
If you can point me to the relevant bits of code to look at I'll have a
go (gulping as I type)

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

[hidden email] <[hidden email]>
Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 2 Dec 2013, at 16:04, Robert Buels <[hidden email]
<[hidden email]>> wrote:

It would be relatively easy to add, but I could use some help.

Any chance you'd want to take a crack at it?


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 11/29/2013 01:49 PM, Keiran Raine wrote:
Hi,

I'm looking to plot lines and points (coverage segmentation data) within
JBrowse.  It seems that a tabix indexed BED file would be appropriate to
do this as it supports single and range based segments as well as a
score value to indicate the vertical position of the value.

As VCF is tabix indexed is this something that could be easily added.

I'm looking for something relatively simple like the following (but most
likely within the same track):




Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

[hidden email] <[hidden email]> <[hidden email]>
Tel:+44 (0)1223 834244 Ext: 7703
Office: H104


-- The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.


------------------------------------------------------------------------------
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into
your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of
AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk



_______________________________________________
Gmod-ajax mailing list
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-- The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.


-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
Rapidly troubleshoot problems before they affect your business. Most IT
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affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
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