[Gmod-ajax] BAM coverage not displaying

classic Classic list List threaded Threaded
6 messages Options
Reply | Threaded
Open this post in threaded view
|

[Gmod-ajax] BAM coverage not displaying

grahammb
Hello all,

Recently I have been working on large BAM files in JBrowse. When I zoom out enough, JBrowse will state "Too much data to show; zoom in to see detail". I realize this takes place when there are too many features on the track to view at a given time.

To address this I created a bigWig file (based off each BAM file) to display coverage data. Each bigWig file, when loaded as their own track, works and displays just fine.

However, when I try to link the bigWig and BAM files, such that the bigWig displays as a coverage for the zoomed out BAM, I cannot seem to get it.

Below is a snippet of my trackList.json:

{
         "label" : "82_1.clean.sorted.bam",
         "key" : "82 1.clean.sorted.bam",
         "category" : "82 BAM",
         "urlTemplate" : "BAMSAM/1.clean.sorted.bam",
         "type" : "JBrowse/View/Track/Alignments2",
         "histograms.urlTemplate" : "coverage/1_coverage.bw",
         "baiUrlTemplate" : "BAMSAM/1.clean.sorted.bam.bai",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "histograms.storeClass" : "JBrowse/Store/SeqFeature/BigWig",
         "type": "Alignments2"
      },

Am I missing something simple here? I have experimented with changing maxFeatureScreenDensity, but obviously eventually the file is too large to render on the screen.

Any help would be greatly appreciated.


Thanks,
Mitchell

------------------------------------------------------------------------------
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

jbrowse_5-09-16.png (190K) Download Attachment
Reply | Threaded
Open this post in threaded view
|

Re: BAM coverage not displaying

Eric Yao
Assuming you do have the maxFeatureScreenDensity option in there, I'm not seeing anything wrong.

You can click the drop menu on the track label and select "Edit Config" to experiment with the configuration in the editor.  Maybe you'll find something.

Sorry, I couldn't provide more insight.

On Mon, May 9, 2016 at 6:54 AM, Graham, Mitchell <[hidden email]> wrote:
Hello all,

Recently I have been working on large BAM files in JBrowse. When I zoom out enough, JBrowse will state "Too much data to show; zoom in to see detail". I realize this takes place when there are too many features on the track to view at a given time.

To address this I created a bigWig file (based off each BAM file) to display coverage data. Each bigWig file, when loaded as their own track, works and displays just fine.

However, when I try to link the bigWig and BAM files, such that the bigWig displays as a coverage for the zoomed out BAM, I cannot seem to get it.

Below is a snippet of my trackList.json:

{
         "label" : "82_1.clean.sorted.bam",
         "key" : "82 1.clean.sorted.bam",
         "category" : "82 BAM",
         "urlTemplate" : "BAMSAM/1.clean.sorted.bam",
         "type" : "JBrowse/View/Track/Alignments2",
         "histograms.urlTemplate" : "coverage/1_coverage.bw",
         "baiUrlTemplate" : "BAMSAM/1.clean.sorted.bam.bai",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "histograms.storeClass" : "JBrowse/Store/SeqFeature/BigWig",
         "type": "Alignments2"
      },

Am I missing something simple here? I have experimented with changing maxFeatureScreenDensity, but obviously eventually the file is too large to render on the screen.

Any help would be greatly appreciated.


Thanks,
Mitchell

------------------------------------------------------------------------------
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax



------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
Reply | Threaded
Open this post in threaded view
|

Re: BAM coverage not displaying

Colin
You probably need to use this type of syntax 

    "histograms": {
        "urlTemplate":"coverage/1_coverage.bw",
        "storeClass" : "JBrowse/Store/SeqFeature/BigWig"
    }

The dot notation is implying that you use this sort of "nested object" rather than actually using the dots in the name

-Colin

On Mon, May 9, 2016 at 6:09 PM, Eric Yao <[hidden email]> wrote:
Assuming you do have the maxFeatureScreenDensity option in there, I'm not seeing anything wrong.

You can click the drop menu on the track label and select "Edit Config" to experiment with the configuration in the editor.  Maybe you'll find something.

Sorry, I couldn't provide more insight.

On Mon, May 9, 2016 at 6:54 AM, Graham, Mitchell <[hidden email]> wrote:
Hello all,

Recently I have been working on large BAM files in JBrowse. When I zoom out enough, JBrowse will state "Too much data to show; zoom in to see detail". I realize this takes place when there are too many features on the track to view at a given time.

To address this I created a bigWig file (based off each BAM file) to display coverage data. Each bigWig file, when loaded as their own track, works and displays just fine.

However, when I try to link the bigWig and BAM files, such that the bigWig displays as a coverage for the zoomed out BAM, I cannot seem to get it.

Below is a snippet of my trackList.json:

{
         "label" : "82_1.clean.sorted.bam",
         "key" : "82 1.clean.sorted.bam",
         "category" : "82 BAM",
         "urlTemplate" : "BAMSAM/1.clean.sorted.bam",
         "type" : "JBrowse/View/Track/Alignments2",
         "histograms.urlTemplate" : "coverage/1_coverage.bw",
         "baiUrlTemplate" : "BAMSAM/1.clean.sorted.bam.bai",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "histograms.storeClass" : "JBrowse/Store/SeqFeature/BigWig",
         "type": "Alignments2"
      },

Am I missing something simple here? I have experimented with changing maxFeatureScreenDensity, but obviously eventually the file is too large to render on the screen.

Any help would be greatly appreciated.


Thanks,
Mitchell

------------------------------------------------------------------------------
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax



------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax



------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
Reply | Threaded
Open this post in threaded view
|

Re: BAM coverage not displaying

grahammb
Dear Colin,

Thank you so much!
This displayed a empty coverage graph though; but I am sure it has to do with the scaling, so I really appreciate your help.

I am however a little confused on when I would use the histograms dot notation.
The documentation online said that it should work:
"Canvas-based feature tracks (CanvasFeatures) support an optional histograms configuration subsection that can contain a definition for a second datastore that holds quantitative data (usually either coverage depth or feature density) to be displayed when zoomed further out than featureScale (or if featureScale is not set, the scale determined by the store's feature density divided by maxFeatureScreenDensity). This is often used for BAM coverage on Alignments2 tracks using the histograms.urlTemplate and histograms.storeClass arguments."

Would you mind explaining when I would use that method?

Thanks again for all your help!

Sincerely,
Mitchell

On Tue, May 10, 2016 at 12:26 PM, Colin <[hidden email]> wrote:
You probably need to use this type of syntax 

    "histograms": {
        "urlTemplate":"coverage/1_coverage.bw",
        "storeClass" : "JBrowse/Store/SeqFeature/BigWig"
    }

The dot notation is implying that you use this sort of "nested object" rather than actually using the dots in the name

-Colin

On Mon, May 9, 2016 at 6:09 PM, Eric Yao <[hidden email]> wrote:
Assuming you do have the maxFeatureScreenDensity option in there, I'm not seeing anything wrong.

You can click the drop menu on the track label and select "Edit Config" to experiment with the configuration in the editor.  Maybe you'll find something.

Sorry, I couldn't provide more insight.

On Mon, May 9, 2016 at 6:54 AM, Graham, Mitchell <[hidden email]> wrote:
Hello all,

Recently I have been working on large BAM files in JBrowse. When I zoom out enough, JBrowse will state "Too much data to show; zoom in to see detail". I realize this takes place when there are too many features on the track to view at a given time.

To address this I created a bigWig file (based off each BAM file) to display coverage data. Each bigWig file, when loaded as their own track, works and displays just fine.

However, when I try to link the bigWig and BAM files, such that the bigWig displays as a coverage for the zoomed out BAM, I cannot seem to get it.

Below is a snippet of my trackList.json:

{
         "label" : "82_1.clean.sorted.bam",
         "key" : "82 1.clean.sorted.bam",
         "category" : "82 BAM",
         "urlTemplate" : "BAMSAM/1.clean.sorted.bam",
         "type" : "JBrowse/View/Track/Alignments2",
         "histograms.urlTemplate" : "coverage/1_coverage.bw",
         "baiUrlTemplate" : "BAMSAM/1.clean.sorted.bam.bai",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "histograms.storeClass" : "JBrowse/Store/SeqFeature/BigWig",
         "type": "Alignments2"
      },

Am I missing something simple here? I have experimented with changing maxFeatureScreenDensity, but obviously eventually the file is too large to render on the screen.

Any help would be greatly appreciated.


Thanks,
Mitchell

------------------------------------------------------------------------------
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax



------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
Reply | Threaded
Open this post in threaded view
|

Re: BAM coverage not displaying

Colin
I guess what might be of interest is that the dot notation actually does work in tracks.conf format files. You can see an example of that for histograms.storeClass and histograms.urlTemplate in the volvox sample data, e.g. sample_data/json/volvox/tracks.conf

The key thing is that tracks.conf and trackList.json express the same types of ideas but in different formats, so in trackList.json, you would use the "nested object" JSON style instead of the dot notation tracks.conf style. The JBrowse configuration guide has an overview of both formats here http://gmod.org/wiki/JBrowse_Configuration_Guide#Configuration_Loading.2C_Files.2C_and_Formats

As far as the scaling issue, I think you can set, for example, histograms.max = 10 to make your coverage track have a max score. The histograms don't perform "local autoscale" like normal bigwig tracks though AFAIK!

Hope that helps

-Colin

On Tue, May 10, 2016 at 11:48 AM, Graham, Mitchell <[hidden email]> wrote:
Dear Colin,

Thank you so much!
This displayed a empty coverage graph though; but I am sure it has to do with the scaling, so I really appreciate your help.

I am however a little confused on when I would use the histograms dot notation.
The documentation online said that it should work:
"Canvas-based feature tracks (CanvasFeatures) support an optional histograms configuration subsection that can contain a definition for a second datastore that holds quantitative data (usually either coverage depth or feature density) to be displayed when zoomed further out than featureScale (or if featureScale is not set, the scale determined by the store's feature density divided by maxFeatureScreenDensity). This is often used for BAM coverage on Alignments2 tracks using the histograms.urlTemplate and histograms.storeClass arguments."

Would you mind explaining when I would use that method?

Thanks again for all your help!

Sincerely,
Mitchell

On Tue, May 10, 2016 at 12:26 PM, Colin <[hidden email]> wrote:
You probably need to use this type of syntax 

    "histograms": {
        "urlTemplate":"coverage/1_coverage.bw",
        "storeClass" : "JBrowse/Store/SeqFeature/BigWig"
    }

The dot notation is implying that you use this sort of "nested object" rather than actually using the dots in the name

-Colin

On Mon, May 9, 2016 at 6:09 PM, Eric Yao <[hidden email]> wrote:
Assuming you do have the maxFeatureScreenDensity option in there, I'm not seeing anything wrong.

You can click the drop menu on the track label and select "Edit Config" to experiment with the configuration in the editor.  Maybe you'll find something.

Sorry, I couldn't provide more insight.

On Mon, May 9, 2016 at 6:54 AM, Graham, Mitchell <[hidden email]> wrote:
Hello all,

Recently I have been working on large BAM files in JBrowse. When I zoom out enough, JBrowse will state "Too much data to show; zoom in to see detail". I realize this takes place when there are too many features on the track to view at a given time.

To address this I created a bigWig file (based off each BAM file) to display coverage data. Each bigWig file, when loaded as their own track, works and displays just fine.

However, when I try to link the bigWig and BAM files, such that the bigWig displays as a coverage for the zoomed out BAM, I cannot seem to get it.

Below is a snippet of my trackList.json:

{
         "label" : "82_1.clean.sorted.bam",
         "key" : "82 1.clean.sorted.bam",
         "category" : "82 BAM",
         "urlTemplate" : "BAMSAM/1.clean.sorted.bam",
         "type" : "JBrowse/View/Track/Alignments2",
         "histograms.urlTemplate" : "coverage/1_coverage.bw",
         "baiUrlTemplate" : "BAMSAM/1.clean.sorted.bam.bai",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "histograms.storeClass" : "JBrowse/Store/SeqFeature/BigWig",
         "type": "Alignments2"
      },

Am I missing something simple here? I have experimented with changing maxFeatureScreenDensity, but obviously eventually the file is too large to render on the screen.

Any help would be greatly appreciated.


Thanks,
Mitchell

------------------------------------------------------------------------------
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax



------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax





------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
Reply | Threaded
Open this post in threaded view
|

Re: BAM coverage not displaying

grahammb
Dear Colin,

Thank you very much for explaining that. I knew that they were different files for the same idea, I did not however know that only certain functions would work with certain file formats.

Thanks for all your assistance.

Sincerely,
Mitchell

On May 10, 2016, at 1:19 PM, Colin <[hidden email]> wrote:

I guess what might be of interest is that the dot notation actually does work in tracks.conf format files. You can see an example of that for histograms.storeClass and histograms.urlTemplate in the volvox sample data, e.g. sample_data/json/volvox/tracks.conf

The key thing is that tracks.conf and trackList.json express the same types of ideas but in different formats, so in trackList.json, you would use the "nested object" JSON style instead of the dot notation tracks.conf style. The JBrowse configuration guide has an overview of both formats here http://gmod.org/wiki/JBrowse_Configuration_Guide#Configuration_Loading.2C_Files.2C_and_Formats

As far as the scaling issue, I think you can set, for example, histograms.max = 10 to make your coverage track have a max score. The histograms don't perform "local autoscale" like normal bigwig tracks though AFAIK!

Hope that helps

-Colin

On Tue, May 10, 2016 at 11:48 AM, Graham, Mitchell <[hidden email]> wrote:
Dear Colin,

Thank you so much!
This displayed a empty coverage graph though; but I am sure it has to do with the scaling, so I really appreciate your help.

I am however a little confused on when I would use the histograms dot notation.
The documentation online said that it should work:
"Canvas-based feature tracks (CanvasFeatures) support an optional histograms configuration subsection that can contain a definition for a second datastore that holds quantitative data (usually either coverage depth or feature density) to be displayed when zoomed further out than featureScale (or if featureScale is not set, the scale determined by the store's feature density divided by maxFeatureScreenDensity). This is often used for BAM coverage on Alignments2 tracks using the histograms.urlTemplate and histograms.storeClass arguments."

Would you mind explaining when I would use that method?

Thanks again for all your help!

Sincerely,
Mitchell

On Tue, May 10, 2016 at 12:26 PM, Colin <[hidden email]> wrote:
You probably need to use this type of syntax 

    "histograms": {
        "urlTemplate":"coverage/1_coverage.bw",
        "storeClass" : "JBrowse/Store/SeqFeature/BigWig"
    }

The dot notation is implying that you use this sort of "nested object" rather than actually using the dots in the name

-Colin

On Mon, May 9, 2016 at 6:09 PM, Eric Yao <[hidden email]> wrote:
Assuming you do have the maxFeatureScreenDensity option in there, I'm not seeing anything wrong.

You can click the drop menu on the track label and select "Edit Config" to experiment with the configuration in the editor.  Maybe you'll find something.

Sorry, I couldn't provide more insight.

On Mon, May 9, 2016 at 6:54 AM, Graham, Mitchell <[hidden email]> wrote:
Hello all,

Recently I have been working on large BAM files in JBrowse. When I zoom out enough, JBrowse will state "Too much data to show; zoom in to see detail". I realize this takes place when there are too many features on the track to view at a given time.

To address this I created a bigWig file (based off each BAM file) to display coverage data. Each bigWig file, when loaded as their own track, works and displays just fine.

However, when I try to link the bigWig and BAM files, such that the bigWig displays as a coverage for the zoomed out BAM, I cannot seem to get it.

Below is a snippet of my trackList.json:

{
         "label" : "82_1.clean.sorted.bam",
         "key" : "82 1.clean.sorted.bam",
         "category" : "82 BAM",
         "urlTemplate" : "BAMSAM/1.clean.sorted.bam",
         "type" : "JBrowse/View/Track/Alignments2",
         "histograms.urlTemplate" : "coverage/1_coverage.bw",
         "baiUrlTemplate" : "BAMSAM/1.clean.sorted.bam.bai",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "histograms.storeClass" : "JBrowse/Store/SeqFeature/BigWig",
         "type": "Alignments2"
      },

Am I missing something simple here? I have experimented with changing maxFeatureScreenDensity, but obviously eventually the file is too large to render on the screen.

Any help would be greatly appreciated.


Thanks,
Mitchell

------------------------------------------------------------------------------
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax



------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax





------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax