[Gmod-ajax] BigWig histograms for BAM files

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[Gmod-ajax] BigWig histograms for BAM files

Keiran Raine
Hi,

Below is a config I'm using to show the histogram of read depth from BigWig once maxFeatureScreenDensity has been reached for the BAM track.

What I odd is that when the display switches to the histogram it is automatically using a scale of 100,000, I think it's showing data but I can't really tell.  I've tried setting 'autoscale' to local using the config editor in the interface but that doesn't seem to have an effect.

Asking for the read count for the region being displayed gives only 5001 reads, all details at the end of this email.

Any ideas?

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

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

[kr2]134: samtools view -c test.bam 1:212286791-212297210
5001
[kr2]135: ls -l test.*
lrwxrwxrwx 1 kr2 cancer 40 Jan  2 16:17 test.bam -> /nfs/cancer_trk-dev03/00000011/11675.bam
lrwxrwxrwx 1 kr2 cancer 44 Jan  2 16:17 test.bam.bai -> /nfs/cancer_trk-dev02/00000003/11676.bam.bai

      {
         "displayMode" : "compact",
         "histograms" : {
            "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
            "urlTemplate" : "nfs/cancer_trk-dev03/00000011/11692.bw"
         },
         "style" : {
            "height" : 7
         },
         "key" : "BWA BAM PD13371a",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "maxFeatureScreenDensity" : 4,
         "urlTemplate" : "nfs/cancer_trk-dev03/00000011/11675.bam",
         "metadata" : {
            "category" : "PD13371",
            "Description" : "Mapped reads from BWA BAM"
         },
         "type" : "JBrowse/View/Track/Alignments2",
         "label" : "PD13371a-BWA BAM",
         "baiUrlTemplate" : "nfs/cancer_trk-dev02/00000003/11676.bam.bai"
      },


-- 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: BigWig histograms for BAM files

Robert Buels-2
The histograms in the CanvasFeatures tracks aren't a real wiggle/xyplot
track, they can't do autoscaling or any of the other fancy things.

Right now, it's using the global max that's recorded in your BigWig
file.  The best I can do before JBrowse 2 is to add support for a
`histograms.max` config value that you can use to set a different max
value manually.  That will come out in 1.11.1, which I'll release next week.

Will that work for now?


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

On 01/02/2014 11:32 AM, Keiran Raine wrote:

> Hi,
>
> Below is a config I'm using to show the histogram of read depth from
> BigWig once maxFeatureScreenDensity has been reached for the BAM track.
>
> What I odd is that when the display switches to the histogram it is
> automatically using a scale of 100,000, I think it's showing data but I
> can't really tell.  I've tried setting 'autoscale' to local using the
> config editor in the interface but that doesn't seem to have an effect.
>
> Asking for the read count for the region being displayed gives only 5001
> reads, all details at the end of this email.
>
> Any ideas?
>
> 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
>
> [kr2]134: samtools view -c test.bam 1:212286791-212297210
> 5001
> [kr2]135: ls -l test.*
> lrwxrwxrwx 1 kr2 cancer 40 Jan  2 16:17 test.bam ->
> /nfs/cancer_trk-dev03/00000011/11675.bam
> lrwxrwxrwx 1 kr2 cancer 44 Jan  2 16:17 test.bam.bai ->
> /nfs/cancer_trk-dev02/00000003/11676.bam.bai
>
>        {
>           "displayMode" : "compact",
>           "histograms" : {
>              "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
>              "urlTemplate" : "nfs/cancer_trk-dev03/00000011/11692.bw"
>           },
>           "style" : {
>              "height" : 7
>           },
>           "key" : "BWA BAM PD13371a",
>           "storeClass" : "JBrowse/Store/SeqFeature/BAM",
>           "maxFeatureScreenDensity" : 4,
>           "urlTemplate" : "nfs/cancer_trk-dev03/00000011/11675.bam",
>           "metadata" : {
>              "category" : "PD13371",
>              "Description" : "Mapped reads from BWA BAM"
>           },
>           "type" : "JBrowse/View/Track/Alignments2",
>           "label" : "PD13371a-BWA BAM",
>           "baiUrlTemplate" : "nfs/cancer_trk-dev02/00000003/11676.bam.bai"
>        },
>
>
> -- 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=84349831&iu=/4140/ostg.clktrk
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

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Re: BigWig histograms for BAM files

Keiran Raine
Hi Robert,

I'm happy for it to be a manual thing for now, will it show that the peak is over the specified value, then I can direct the user to modify the config if they need to see it in more detail.

Thanks,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

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

On 3 Jan 2014, at 06:46, Robert Buels <[hidden email]> wrote:

The histograms in the CanvasFeatures tracks aren't a real wiggle/xyplot track, they can't do autoscaling or any of the other fancy things.

Right now, it's using the global max that's recorded in your BigWig file.  The best I can do before JBrowse 2 is to add support for a `histograms.max` config value that you can use to set a different max value manually.  That will come out in 1.11.1, which I'll release next week.

Will that work for now?


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

On 01/02/2014 11:32 AM, Keiran Raine wrote:
Hi,

Below is a config I'm using to show the histogram of read depth from
BigWig once maxFeatureScreenDensity has been reached for the BAM track.

What I odd is that when the display switches to the histogram it is
automatically using a scale of 100,000, I think it's showing data but I
can't really tell.  I've tried setting 'autoscale' to local using the
config editor in the interface but that doesn't seem to have an effect.

Asking for the read count for the region being displayed gives only 5001
reads, all details at the end of this email.

Any ideas?

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

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

[kr2]134: samtools view -c test.bam 1:212286791-212297210
5001
[kr2]135: ls -l test.*
lrwxrwxrwx 1 kr2 cancer 40 Jan  2 16:17 test.bam ->
/nfs/cancer_trk-dev03/00000011/11675.bam
lrwxrwxrwx 1 kr2 cancer 44 Jan  2 16:17 test.bam.bai ->
/nfs/cancer_trk-dev02/00000003/11676.bam.bai

      {
         "displayMode" : "compact",
         "histograms" : {
            "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
            "urlTemplate" : "nfs/cancer_trk-dev03/00000011/11692.bw"
         },
         "style" : {
            "height" : 7
         },
         "key" : "BWA BAM PD13371a",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "maxFeatureScreenDensity" : 4,
         "urlTemplate" : "nfs/cancer_trk-dev03/00000011/11675.bam",
         "metadata" : {
            "category" : "PD13371",
            "Description" : "Mapped reads from BWA BAM"
         },
         "type" : "JBrowse/View/Track/Alignments2",
         "label" : "PD13371a-BWA BAM",
         "baiUrlTemplate" : "nfs/cancer_trk-dev02/00000003/11676.bam.bai"
      },


-- 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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-- 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: BigWig histograms for BAM files

Robert Buels-2
It doesn't do the little red band at the top on overflow, but I'll add
that in 1.11.1.  https://github.com/GMOD/jbrowse/issues/402


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

On 01/03/2014 05:40 AM, Keiran Raine wrote:

> Hi Robert,
>
> I'm happy for it to be a manual thing for now, will it show that the
> peak is over the specified value, then I can direct the user to modify
> the config if they need to see it in more detail.
>
> Thanks,
>
> 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 3 Jan 2014, at 06:46, Robert Buels <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>> The histograms in the CanvasFeatures tracks aren't a real
>> wiggle/xyplot track, they can't do autoscaling or any of the other
>> fancy things.
>>
>> Right now, it's using the global max that's recorded in your BigWig
>> file.  The best I can do before JBrowse 2 is to add support for a
>> `histograms.max` config value that you can use to set a different max
>> value manually.  That will come out in 1.11.1, which I'll release next
>> week.
>>
>> Will that work for now?
>>
>>
>> Robert Buels
>> Lead Developer
>> JBrowse - http://jbrowse.org
>>
>> On 01/02/2014 11:32 AM, Keiran Raine wrote:
>>> Hi,
>>>
>>> Below is a config I'm using to show the histogram of read depth from
>>> BigWig once maxFeatureScreenDensity has been reached for the BAM track.
>>>
>>> What I odd is that when the display switches to the histogram it is
>>> automatically using a scale of 100,000, I think it's showing data but I
>>> can't really tell.  I've tried setting 'autoscale' to local using the
>>> config editor in the interface but that doesn't seem to have an effect.
>>>
>>> Asking for the read count for the region being displayed gives only 5001
>>> reads, all details at the end of this email.
>>>
>>> Any ideas?
>>>
>>> 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
>>>
>>> [kr2]134: samtools view -c test.bam 1:212286791-212297210
>>> 5001
>>> [kr2]135: ls -l test.*
>>> lrwxrwxrwx 1 kr2 cancer 40 Jan  2 16:17 test.bam ->
>>> /nfs/cancer_trk-dev03/00000011/11675.bam
>>> lrwxrwxrwx 1 kr2 cancer 44 Jan  2 16:17 test.bam.bai ->
>>> /nfs/cancer_trk-dev02/00000003/11676.bam.bai
>>>
>>>       {
>>>          "displayMode" : "compact",
>>>          "histograms" : {
>>>             "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
>>>             "urlTemplate" : "nfs/cancer_trk-dev03/00000011/11692.bw"
>>>          },
>>>          "style" : {
>>>             "height" : 7
>>>          },
>>>          "key" : "BWA BAM PD13371a",
>>>          "storeClass" : "JBrowse/Store/SeqFeature/BAM",
>>>          "maxFeatureScreenDensity" : 4,
>>>          "urlTemplate" : "nfs/cancer_trk-dev03/00000011/11675.bam",
>>>          "metadata" : {
>>>             "category" : "PD13371",
>>>             "Description" : "Mapped reads from BWA BAM"
>>>          },
>>>          "type" : "JBrowse/View/Track/Alignments2",
>>>          "label" : "PD13371a-BWA BAM",
>>>          "baiUrlTemplate" : "nfs/cancer_trk-dev02/00000003/11676.bam.bai"
>>>       },
>>>
>>>
>>> -- 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=84349831&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.

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