[Gmod-ajax] Colour reads from a BAM file

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[Gmod-ajax] Colour reads from a BAM file

James Morris
Hello,

I am using Jbrowse to view some RNAseq data just on my local machine.

Is it possible to colour the reads in a single track differently based on information I have in the id.

I have 256 different classes (based on a 4bp sequence) so simply creating separate tracks for each class would not work as there would be too many tracks to view at once.

If I could colour the reads I think it will be easy to visualise the distribution of the different classes at points where the reads pileup.

Any help on this would be great.

Thanks,

James

--
 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: Colour reads from a BAM file

James Casbon
I'd like to see this as well.  My preference would be to assign
colours based on the read group annotations in the BAM file.

On 8 October 2010 11:52, James Morris <[hidden email]> wrote:

> Hello,
>
> I am using Jbrowse to view some RNAseq data just on my local machine.
>
> Is it possible to colour the reads in a single track differently based on information I have in the id.
>
> I have 256 different classes (based on a 4bp sequence) so simply creating separate tracks for each class would not work as there would be too many tracks to view at once.
>
> If I could colour the reads I think it will be easy to visualise the distribution of the different classes at points where the reads pileup.
>
> Any help on this would be great.
>
> Thanks,
>
> James
>
> --
>  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.
>
> ------------------------------------------------------------------------------
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
> Spend less time writing and  rewriting code and more time creating great
> experiences on the web. Be a part of the beta today.
> http://p.sf.net/sfu/beautyoftheweb
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

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standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
Spend less time writing and  rewriting code and more time creating great
experiences on the web. Be a part of the beta today.
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Re: Colour reads from a BAM file

Mitch Skinner
  The current plan for this is to allow the user to specify a javascript
function that gets called when features get put on screen, and can
change the CSS style of a feature based on the feature data (which could
include the ID, or whatever other information is in the JSON.

I've been experimenting with this lately; for example, in
ucsc-to-json.pl there's a bit of perl that specifies a javascript
callback, but it will be possible to specify that on the command line
for flatfile-to-json.pl or in a config file for biodb-to-json.pl:

==========
     my $color = sprintf("#%02x%02x%02x",
                         $track->{colorR},
                         $track->{colorG},
                         $track->{colorB});

     if ($subfeatures) {
         $style{subfeatureHeaders} = \@subfeatHeaders;
         $style{class} = "generic_parent";
         $style{clientConfig}->{featureCallback} = <<ENDJS;
function(feat, fields, div) {
     if (fields.type) {
         div.className = "basic";
         switch (feat[fields.type]) {
         case "CDS":
         case "thick":
             div.style.height = "10px";
             div.style.marginTop = "-3px";
             break;
         case "UTR":
         case "thin":
             div.style.height = "6px";
             div.style.marginTop = "-1px";
             break;
         }
         div.style.backgroundColor = "$color";
     }
}
ENDJS
     }
==========

Currently, the callback gets the feature data, the "fields" object that
specifies what's in the feature data, and the actual HTML element that
will represent the feature.  That's not necessarily the final interface,
but it's what I'm currently experimenting with.

This option should make it into the next release in December, but for
now it's just work-in-progress.  On the plus side, if you have opinions
about how it should work, now's your chance to weigh in :)

Mitch

On 10/08/2010 04:09 AM, James Casbon wrote:

> I'd like to see this as well.  My preference would be to assign
> colours based on the read group annotations in the BAM file.
>
> On 8 October 2010 11:52, James Morris<[hidden email]>  wrote:
>> Hello,
>>
>> I am using Jbrowse to view some RNAseq data just on my local machine.
>>
>> Is it possible to colour the reads in a single track differently based on information I have in the id.
>>
>> I have 256 different classes (based on a 4bp sequence) so simply creating separate tracks for each class would not work as there would be too many tracks to view at once.
>>
>> If I could colour the reads I think it will be easy to visualise the distribution of the different classes at points where the reads pileup.
>>
>> Any help on this would be great.
>>
>> Thanks,
>>
>> James
>>
>> --
>>   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.
>>
>> ------------------------------------------------------------------------------
>> Beautiful is writing same markup. Internet Explorer 9 supports
>> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2&  L3.
>> Spend less time writing and  rewriting code and more time creating great
>> experiences on the web. Be a part of the beta today.
>> http://p.sf.net/sfu/beautyoftheweb
>> _______________________________________________
>> Gmod-ajax mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
> ------------------------------------------------------------------------------
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2&  L3.
> Spend less time writing and  rewriting code and more time creating great
> experiences on the web. Be a part of the beta today.
> http://p.sf.net/sfu/beautyoftheweb
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax


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