GBrowse Subtracks

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GBrowse Subtracks

empyrean
Hi.. i have Mapping data for 3 different tissues. I mapped to soybean genome. I converted bam to bedgraph to bigwig. Now i have bigwig files for 3 tissues. i am trying to upload to gbrowse using subtracks. I can see the subtracks track and popup but no data is pulling from  my metadata file.

please correct me where i am doing wrong.

I have attached a screenshot from soybase showing subtracks of transcript density for different tissues. i need to get my bigwigs in to similar format.

###Conf file #####

[soy_test]
feature  = summary
category = Reads
feature  = coverage
database = soy_atlas_test
glyph    = wiggle_density
height = 30
bicolor_pivot = 20
pos_color = blue
neg_color = red
key       = soyatlas read density
bump  = overlap
opacity = 0.5
subtrack select  = Tissue tag_value tissue
subtrack table   = Sample_3 *;
                   Sample_4 *;
                   Sample_5 *;
scale = both

###metafile####
[Sample_3.bw]
display_name = "Leaf"
method       = Sample_3

[Sample_4.bw]
display_name = "Root"
method       = Sample_4

[Sample_5.bw]
display_name = "Seed"
method       = Sample_5





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Re: GBrowse Subtracks

Timothy Parnell
Hi,

I see a couple of things.

First, you have a duplicate feature line in the conf stanza, which means it will use the last one. You should just use the summary feature (the coverage feature won't be recognized by the database adaptor). By the way, you are using the Bio::DB::BigWigSet adaptor, right?

Second, the subtrack select needs to have a valid method or attribute to filter. The metadata file does not list a tissue attribute. But since you have both "display_name" and "method" attributes, you can simply use those for your selection. So set
subtrack select = method

I think that will work.

Tim

On Sep 18, 2013, at 10:07 AM, empyrean999 <[hidden email]> wrote:

> Hi.. i have Mapping data for 3 different tissues. I mapped to soybean genome. I converted bam to bedgraph to bigwig. Now i have bigwig files for 3 tissues. i am trying to upload to gbrowse using subtracks. I can see the subtracks track and popup but no data is pulling from  my metadata file.
>
> please correct me where i am doing wrong.
>
> I have attached a screenshot from soybase showing subtracks of transcript density for different tissues. i need to get my bigwigs in to similar format.
>
> ###Conf file #####
>
> [soy_test]
> feature  = summary
> category = Reads
> feature  = coverage
> database = soy_atlas_test
> glyph    = wiggle_density
> height = 30
> bicolor_pivot = 20
> pos_color = blue
> neg_color = red
> key       = soyatlas read density
> bump  = overlap
> opacity = 0.5
> subtrack select  = Tissue tag_value tissue
> subtrack table   = Sample_3 *;
>                    Sample_4 *;
>                    Sample_5 *;
> scale = both
>
> ###metafile####
> [Sample_3.bw]
> display_name = "Leaf"
> method       = Sample_3
>
> [Sample_4.bw]
> display_name = "Root"
> method       = Sample_4
>
> [Sample_5.bw]
> display_name = "Seed"
> method       = Sample_5
>
>
>
>
> <soybase_subtracks.PNG>------------------------------------------------------------------------------
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Fwd: GBrowse Subtracks

empyrean

Thank you for your prompt response, Tim.

I did changed feature to summary, subtract select = method and i am using bigwigset adaptor. After modifying them, my conf and meta data files looks like this. 

[soy_test:database]
db_adaptor    = Bio::DB::BigWigSet
db_args       = -dir /home/soybean/bigwig
search options = none


[soy_atlas_test]
feature  = summary
category = Test
database = soy_atlas_test
glyph    = wiggle_density
height = 30
bicolor_pivot = 20
pos_color = blue
neg_color = red
key       = soyatlas read density
bump  = overlap
opacity = 0.5
subtrack select  = method
subtrack table   = Sample_3 *;
                   Sample_4 *;
                   Sample_5 *;

###meta data####

[Sample_3.bw]
display_name = "root"
method       = Sample_3

[Sample_4.bw]
display_name = "shoot"
method       = Sample_4

[Sample_5.bw]
display_name = "seed"
method       = Sample_5


But i am getting some error at track " Track Rendering error : Not a code reference at (eval 116) line 6 " Attached the figure below.. 

When i looked at error log file, i see the following things.

Use of uninitialized value in string eq at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 322
 Use of uninitialized value in concatenation (.) or string at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 326.
Use of uninitialized value in string eq at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 315.
Use of uninitialized value in string eq at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 322.,
Use of uninitialized value in concatenation (.) or string at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 326., referer: 
Use of uninitialized value in exists at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2.pm line 395.


Thanks again for your support and help !



On Wed, Sep 18, 2013 at 12:41 PM, Timothy Parnell <[hidden email]> wrote:
Hi,

I see a couple of things.

First, you have a duplicate feature line in the conf stanza, which means it will use the last one. You should just use the summary feature (the coverage feature won't be recognized by the database adaptor). By the way, you are using the Bio::DB::BigWigSet adaptor, right?

Second, the subtrack select needs to have a valid method or attribute to filter. The metadata file does not list a tissue attribute. But since you have both "display_name" and "method" attributes, you can simply use those for your selection. So set
subtrack select = method

I think that will work.

Tim

On Sep 18, 2013, at 10:07 AM, empyrean999 <[hidden email]> wrote:

> Hi.. i have Mapping data for 3 different tissues. I mapped to soybean genome. I converted bam to bedgraph to bigwig. Now i have bigwig files for 3 tissues. i am trying to upload to gbrowse using subtracks. I can see the subtracks track and popup but no data is pulling from  my metadata file.
>
> please correct me where i am doing wrong.
>
> I have attached a screenshot from soybase showing subtracks of transcript density for different tissues. i need to get my bigwigs in to similar format.
>
> ###Conf file #####
>
> [soy_test]
> feature  = summary
> category = Reads
> feature  = coverage
> database = soy_atlas_test
> glyph    = wiggle_density
> height = 30
> bicolor_pivot = 20
> pos_color = blue
> neg_color = red
> key       = soyatlas read density
> bump  = overlap
> opacity = 0.5
> subtrack select  = Tissue tag_value tissue
> subtrack table   = Sample_3 *;
>                    Sample_4 *;
>                    Sample_5 *;
> scale = both
>
> ###metafile####
> [Sample_3.bw]
> display_name = "Leaf"
> method       = Sample_3
>
> [Sample_4.bw]
> display_name = "Root"
> method       = Sample_4
>
> [Sample_5.bw]
> display_name = "Seed"
> method       = Sample_5
>
>
>
>
> <soybase_subtracks.PNG>------------------------------------------------------------------------------
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Re: Fwd: GBrowse Subtracks

Timothy Parnell
Ah, my mistake.

The subtrack select requires two values, delimited by space, a human-interpretable label and then the feature method. So, it should be, for example,

subtrack select = Sample method

Tim

On Sep 18, 2013, at 11:20 AM, empyrean999 <[hidden email]<mailto:[hidden email]>>
 wrote:


Thank you for your prompt response, Tim.

I did changed feature to summary, subtract select = method and i am using bigwigset adaptor. After modifying them, my conf and meta data files looks like this.

[soy_test:database]
db_adaptor    = Bio::DB::BigWigSet
db_args       = -dir /home/soybean/bigwig
search options = none


[soy_atlas_test]
feature  = summary
category = Test
database = soy_atlas_test
glyph    = wiggle_density
height = 30
bicolor_pivot = 20
pos_color = blue
neg_color = red
key       = soyatlas read density
bump  = overlap
opacity = 0.5
subtrack select  = method
subtrack table   = Sample_3 *;
                   Sample_4 *;
                   Sample_5 *;

###meta data####

[Sample_3.bw]
display_name = "root"
method       = Sample_3

[Sample_4.bw]
display_name = "shoot"
method       = Sample_4

[Sample_5.bw]
display_name = "seed"
method       = Sample_5


But i am getting some error at track " Track Rendering error : Not a code reference at (eval 116) line 6 " Attached the figure below..

When i looked at error log file, i see the following things.

Use of uninitialized value in string eq at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 322
 Use of uninitialized value in concatenation (.) or string at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 326.
Use of uninitialized value in string eq at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 315.
Use of uninitialized value in string eq at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 322.,
Use of uninitialized value in concatenation (.) or string at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 326., referer:
Use of uninitialized value in exists at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2.pm line 395.


Thanks again for your support and help !



On Wed, Sep 18, 2013 at 12:41 PM, Timothy Parnell <[hidden email]<mailto:[hidden email]>> wrote:
Hi,

I see a couple of things.

First, you have a duplicate feature line in the conf stanza, which means it will use the last one. You should just use the summary feature (the coverage feature won't be recognized by the database adaptor). By the way, you are using the Bio::DB::BigWigSet adaptor, right?

Second, the subtrack select needs to have a valid method or attribute to filter. The metadata file does not list a tissue attribute. But since you have both "display_name" and "method" attributes, you can simply use those for your selection. So set
subtrack select = method

I think that will work.

Tim

On Sep 18, 2013, at 10:07 AM, empyrean999 <[hidden email]<mailto:[hidden email]>> wrote:

> Hi.. i have Mapping data for 3 different tissues. I mapped to soybean genome. I converted bam to bedgraph to bigwig. Now i have bigwig files for 3 tissues. i am trying to upload to gbrowse using subtracks. I can see the subtracks track and popup but no data is pulling from  my metadata file.
>
> please correct me where i am doing wrong.
>
> I have attached a screenshot from soybase showing subtracks of transcript density for different tissues. i need to get my bigwigs in to similar format.
>
> ###Conf file #####
>
> [soy_test]
> feature  = summary
> category = Reads
> feature  = coverage
> database = soy_atlas_test
> glyph    = wiggle_density
> height = 30
> bicolor_pivot = 20
> pos_color = blue
> neg_color = red
> key       = soyatlas read density
> bump  = overlap
> opacity = 0.5
> subtrack select  = Tissue tag_value tissue
> subtrack table   = Sample_3 *;
>                    Sample_4 *;
>                    Sample_5 *;
> scale = both
>
> ###metafile####
> [Sample_3.bw]
> display_name = "Leaf"
> method       = Sample_3
>
> [Sample_4.bw]
> display_name = "Root"
> method       = Sample_4
>
> [Sample_5.bw]
> display_name = "Seed"
> method       = Sample_5
>
>
>
>
> <soybase_subtracks.PNG>------------------------------------------------------------------------------
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> http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk_______________________________________________
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> [hidden email]<mailto:[hidden email]>
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse



<soy_error.PNG>------------------------------------------------------------------------------
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Re: Fwd: GBrowse Subtracks

empyrean
Thank you Tim, 

I made the change for "subtract select = Sample method" . That took care of error. but again its still blank and i dont see the tracks in the browser. To quality check the data, i added a track from sample_3 as seperate bigwig file and it worked fine with out any issues. i am attaching the figure with sample_ 3 track and blank subtracks. The data is there but its just that i am missing something here. Can you think of any changes i can make to get this working?

i got some errors while loading as well.  mostly this one. i dont know whether this is related to our data or not but just pasting here..
"Use of uninitialized value in exists at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2.pm line 395."


On Wed, Sep 18, 2013 at 1:54 PM, Timothy Parnell <[hidden email]> wrote:
Ah, my mistake.

The subtrack select requires two values, delimited by space, a human-interpretable label and then the feature method. So, it should be, for example,

subtrack select = Sample method

Tim

On Sep 18, 2013, at 11:20 AM, empyrean999 <[hidden email]<mailto:[hidden email]>>
 wrote:


Thank you for your prompt response, Tim.

I did changed feature to summary, subtract select = method and i am using bigwigset adaptor. After modifying them, my conf and meta data files looks like this.

[soy_test:database]
db_adaptor    = Bio::DB::BigWigSet
db_args       = -dir /home/soybean/bigwig
search options = none


[soy_atlas_test]
feature  = summary
category = Test
database = soy_atlas_test
glyph    = wiggle_density
height = 30
bicolor_pivot = 20
pos_color = blue
neg_color = red
key       = soyatlas read density
bump  = overlap
opacity = 0.5
subtrack select  = method
subtrack table   = Sample_3 *;
                   Sample_4 *;
                   Sample_5 *;

###meta data####

[Sample_3.bw]
display_name = "root"
method       = Sample_3

[Sample_4.bw]
display_name = "shoot"
method       = Sample_4

[Sample_5.bw]
display_name = "seed"
method       = Sample_5


But i am getting some error at track " Track Rendering error : Not a code reference at (eval 116) line 6 " Attached the figure below..

When i looked at error log file, i see the following things.

Use of uninitialized value in string eq at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 322
 Use of uninitialized value in concatenation (.) or string at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 326.
Use of uninitialized value in string eq at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 315.
Use of uninitialized value in string eq at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 322.,
Use of uninitialized value in concatenation (.) or string at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 326., referer:
Use of uninitialized value in exists at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2.pm line 395.


Thanks again for your support and help !



On Wed, Sep 18, 2013 at 12:41 PM, Timothy Parnell <[hidden email]<mailto:[hidden email]>> wrote:
Hi,

I see a couple of things.

First, you have a duplicate feature line in the conf stanza, which means it will use the last one. You should just use the summary feature (the coverage feature won't be recognized by the database adaptor). By the way, you are using the Bio::DB::BigWigSet adaptor, right?

Second, the subtrack select needs to have a valid method or attribute to filter. The metadata file does not list a tissue attribute. But since you have both "display_name" and "method" attributes, you can simply use those for your selection. So set
subtrack select = method

I think that will work.

Tim

On Sep 18, 2013, at 10:07 AM, empyrean999 <[hidden email]<mailto:[hidden email]>> wrote:

> Hi.. i have Mapping data for 3 different tissues. I mapped to soybean genome. I converted bam to bedgraph to bigwig. Now i have bigwig files for 3 tissues. i am trying to upload to gbrowse using subtracks. I can see the subtracks track and popup but no data is pulling from  my metadata file.
>
> please correct me where i am doing wrong.
>
> I have attached a screenshot from soybase showing subtracks of transcript density for different tissues. i need to get my bigwigs in to similar format.
>
> ###Conf file #####
>
> [soy_test]
> feature  = summary
> category = Reads
> feature  = coverage
> database = soy_atlas_test
> glyph    = wiggle_density
> height = 30
> bicolor_pivot = 20
> pos_color = blue
> neg_color = red
> key       = soyatlas read density
> bump  = overlap
> opacity = 0.5
> subtrack select  = Tissue tag_value tissue
> subtrack table   = Sample_3 *;
>                    Sample_4 *;
>                    Sample_5 *;
> scale = both
>
> ###metafile####
> [Sample_3.bw]
> display_name = "Leaf"
> method       = Sample_3
>
> [Sample_4.bw]
> display_name = "Root"
> method       = Sample_4
>
> [Sample_5.bw]
> display_name = "Seed"
> method       = Sample_5
>
>
>
>
> <soybase_subtracks.PNG>------------------------------------------------------------------------------
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<soy_error.PNG>------------------------------------------------------------------------------
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Re: GBrowse Subtracks

Timothy Parnell
In reply to this post by Timothy Parnell
Try taking out the bump and opacity options. I don't think the transparency overlap works with the wiggle_density glyph. I know it does not work with wiggle_whiskers, but works perfectly well with wiggle_xyplot.

Also, as a reminder, when troubleshooting, make sure to navigate to different coordinates to avoid cache issues.


On Sep 18, 2013, at 11:54 AM, Timothy Parnell <[hidden email]> wrote:

> Ah, my mistake.
>
> The subtrack select requires two values, delimited by space, a human-interpretable label and then the feature method. So, it should be, for example,
>
> subtrack select = Sample method
>
> Tim
>
> On Sep 18, 2013, at 11:20 AM, empyrean999 <[hidden email]<mailto:[hidden email]>>
> wrote:
>
>
> Thank you for your prompt response, Tim.
>
> I did changed feature to summary, subtract select = method and i am using bigwigset adaptor. After modifying them, my conf and meta data files looks like this.
>
> [soy_test:database]
> db_adaptor    = Bio::DB::BigWigSet
> db_args       = -dir /home/soybean/bigwig
> search options = none
>
>
> [soy_atlas_test]
> feature  = summary
> category = Test
> database = soy_atlas_test
> glyph    = wiggle_density
> height = 30
> bicolor_pivot = 20
> pos_color = blue
> neg_color = red
> key       = soyatlas read density
> bump  = overlap
> opacity = 0.5
> subtrack select  = method
> subtrack table   = Sample_3 *;
>                   Sample_4 *;
>                   Sample_5 *;
>
> ###meta data####
>
> [Sample_3.bw]
> display_name = "root"
> method       = Sample_3
>
> [Sample_4.bw]
> display_name = "shoot"
> method       = Sample_4
>
> [Sample_5.bw]
> display_name = "seed"
> method       = Sample_5
>
>
> But i am getting some error at track " Track Rendering error : Not a code reference at (eval 116) line 6 " Attached the figure below..
>
> When i looked at error log file, i see the following things.
>
> Use of uninitialized value in string eq at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 322
> Use of uninitialized value in concatenation (.) or string at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 326.
> Use of uninitialized value in string eq at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 315.
> Use of uninitialized value in string eq at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 322.,
> Use of uninitialized value in concatenation (.) or string at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 326., referer:
> Use of uninitialized value in exists at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2.pm line 395.
>
>
> Thanks again for your support and help !
>
>
>
> On Wed, Sep 18, 2013 at 12:41 PM, Timothy Parnell <[hidden email]<mailto:[hidden email]>> wrote:
> Hi,
>
> I see a couple of things.
>
> First, you have a duplicate feature line in the conf stanza, which means it will use the last one. You should just use the summary feature (the coverage feature won't be recognized by the database adaptor). By the way, you are using the Bio::DB::BigWigSet adaptor, right?
>
> Second, the subtrack select needs to have a valid method or attribute to filter. The metadata file does not list a tissue attribute. But since you have both "display_name" and "method" attributes, you can simply use those for your selection. So set
> subtrack select = method
>
> I think that will work.
>
> Tim
>
> On Sep 18, 2013, at 10:07 AM, empyrean999 <[hidden email]<mailto:[hidden email]>> wrote:
>
>> Hi.. i have Mapping data for 3 different tissues. I mapped to soybean genome. I converted bam to bedgraph to bigwig. Now i have bigwig files for 3 tissues. i am trying to upload to gbrowse using subtracks. I can see the subtracks track and popup but no data is pulling from  my metadata file.
>>
>> please correct me where i am doing wrong.
>>
>> I have attached a screenshot from soybase showing subtracks of transcript density for different tissues. i need to get my bigwigs in to similar format.
>>
>> ###Conf file #####
>>
>> [soy_test]
>> feature  = summary
>> category = Reads
>> feature  = coverage
>> database = soy_atlas_test
>> glyph    = wiggle_density
>> height = 30
>> bicolor_pivot = 20
>> pos_color = blue
>> neg_color = red
>> key       = soyatlas read density
>> bump  = overlap
>> opacity = 0.5
>> subtrack select  = Tissue tag_value tissue
>> subtrack table   = Sample_3 *;
>>                   Sample_4 *;
>>                   Sample_5 *;
>> scale = both
>>
>> ###metafile####
>> [Sample_3.bw]
>> display_name = "Leaf"
>> method       = Sample_3
>>
>> [Sample_4.bw]
>> display_name = "Root"
>> method       = Sample_4
>>
>> [Sample_5.bw]
>> display_name = "Seed"
>> method       = Sample_5
>>
>>
>>
>>
>> <soybase_subtracks.PNG>------------------------------------------------------------------------------
>> LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99!
>> 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint
>> 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes
>> Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13.
>> http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk_______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]<mailto:[hidden email]>
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
> <soy_error.PNG>------------------------------------------------------------------------------
> LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99!
> 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint
> 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes
> Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13.
> http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk_______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
> ------------------------------------------------------------------------------
> LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99!
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> http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk
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Re: GBrowse Subtracks

empyrean
I took those options. Before that, i tried changing from wiggle_density to wiggle_xyplot also.. no change.. when deselect subtracks and clicked "change" it seems to load but still blank track but the when i open the subtracks popup again, they seem to select by themselves. I removed * after subtrack table also still behaving the same way. 

Errors from log file : 

"Undefined subroutine &JSON::from_json called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 766."
"Premature end of script headers: gbrowse"

Does they mean, am i missing any libraries or required files for subtrack in gbrowse? my gbrowse version is 2.23. will that have any effect?  


while troubleshooting, i am emptying cache from browser everytime as well.. 




On Wed, Sep 18, 2013 at 3:28 PM, Timothy Parnell <[hidden email]> wrote:
Try taking out the bump and opacity options. I don't think the transparency overlap works with the wiggle_density glyph. I know it does not work with wiggle_whiskers, but works perfectly well with wiggle_xyplot.

Also, as a reminder, when troubleshooting, make sure to navigate to different coordinates to avoid cache issues.


On Sep 18, 2013, at 11:54 AM, Timothy Parnell <[hidden email]> wrote:

> Ah, my mistake.
>
> The subtrack select requires two values, delimited by space, a human-interpretable label and then the feature method. So, it should be, for example,
>
> subtrack select = Sample method
>
> Tim
>
> On Sep 18, 2013, at 11:20 AM, empyrean999 <[hidden email]<mailto:[hidden email]>>
> wrote:
>
>
> Thank you for your prompt response, Tim.
>
> I did changed feature to summary, subtract select = method and i am using bigwigset adaptor. After modifying them, my conf and meta data files looks like this.
>
> [soy_test:database]
> db_adaptor    = Bio::DB::BigWigSet
> db_args       = -dir /home/soybean/bigwig
> search options = none
>
>
> [soy_atlas_test]
> feature  = summary
> category = Test
> database = soy_atlas_test
> glyph    = wiggle_density
> height = 30
> bicolor_pivot = 20
> pos_color = blue
> neg_color = red
> key       = soyatlas read density
> bump  = overlap
> opacity = 0.5
> subtrack select  = method
> subtrack table   = Sample_3 *;
>                   Sample_4 *;
>                   Sample_5 *;
>
> ###meta data####
>
> [Sample_3.bw]
> display_name = "root"
> method       = Sample_3
>
> [Sample_4.bw]
> display_name = "shoot"
> method       = Sample_4
>
> [Sample_5.bw]
> display_name = "seed"
> method       = Sample_5
>
>
> But i am getting some error at track " Track Rendering error : Not a code reference at (eval 116) line 6 " Attached the figure below..
>
> When i looked at error log file, i see the following things.
>
> Use of uninitialized value in string eq at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 322
> Use of uninitialized value in concatenation (.) or string at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 326.
> Use of uninitialized value in string eq at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 315.
> Use of uninitialized value in string eq at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 322.,
> Use of uninitialized value in concatenation (.) or string at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 326., referer:
> Use of uninitialized value in exists at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2.pm line 395.
>
>
> Thanks again for your support and help !
>
>
>
> On Wed, Sep 18, 2013 at 12:41 PM, Timothy Parnell <[hidden email]<mailto:[hidden email]>> wrote:
> Hi,
>
> I see a couple of things.
>
> First, you have a duplicate feature line in the conf stanza, which means it will use the last one. You should just use the summary feature (the coverage feature won't be recognized by the database adaptor). By the way, you are using the Bio::DB::BigWigSet adaptor, right?
>
> Second, the subtrack select needs to have a valid method or attribute to filter. The metadata file does not list a tissue attribute. But since you have both "display_name" and "method" attributes, you can simply use those for your selection. So set
> subtrack select = method
>
> I think that will work.
>
> Tim
>
> On Sep 18, 2013, at 10:07 AM, empyrean999 <[hidden email]<mailto:[hidden email]>> wrote:
>
>> Hi.. i have Mapping data for 3 different tissues. I mapped to soybean genome. I converted bam to bedgraph to bigwig. Now i have bigwig files for 3 tissues. i am trying to upload to gbrowse using subtracks. I can see the subtracks track and popup but no data is pulling from  my metadata file.
>>
>> please correct me where i am doing wrong.
>>
>> I have attached a screenshot from soybase showing subtracks of transcript density for different tissues. i need to get my bigwigs in to similar format.
>>
>> ###Conf file #####
>>
>> [soy_test]
>> feature  = summary
>> category = Reads
>> feature  = coverage
>> database = soy_atlas_test
>> glyph    = wiggle_density
>> height = 30
>> bicolor_pivot = 20
>> pos_color = blue
>> neg_color = red
>> key       = soyatlas read density
>> bump  = overlap
>> opacity = 0.5
>> subtrack select  = Tissue tag_value tissue
>> subtrack table   = Sample_3 *;
>>                   Sample_4 *;
>>                   Sample_5 *;
>> scale = both
>>
>> ###metafile####
>> [Sample_3.bw]
>> display_name = "Leaf"
>> method       = Sample_3
>>
>> [Sample_4.bw]
>> display_name = "Root"
>> method       = Sample_4
>>
>> [Sample_5.bw]
>> display_name = "Seed"
>> method       = Sample_5
>>
>>
>>
>>
>> <soybase_subtracks.PNG>------------------------------------------------------------------------------
>> LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99!
>> 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint
>> 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes
>> Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13.
>> http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk_______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]<mailto:[hidden email]>
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
> <soy_error.PNG>------------------------------------------------------------------------------
> LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99!
> 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint
> 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes
> Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13.
> http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk_______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
> ------------------------------------------------------------------------------
> LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99!
> 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint
> 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes
> Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13.
> http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk
> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse



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2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes
Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13.
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Re: GBrowse Subtracks

Scott Cain
Hi,

The undefined subroutine may indicate that, while you might have the JSON module installed, it might be old so that the version you have might not have the from_json method, or JSON isn't installed at all; either way, check into updating it.

Additionally, 2.23 is a really old version of GBrowse, which will make troubleshooting it really difficult.  Would it be possible to upgrade to something newer?

Scott



On Wed, Sep 18, 2013 at 4:02 PM, empyrean999 <[hidden email]> wrote:
I took those options. Before that, i tried changing from wiggle_density to wiggle_xyplot also.. no change.. when deselect subtracks and clicked "change" it seems to load but still blank track but the when i open the subtracks popup again, they seem to select by themselves. I removed * after subtrack table also still behaving the same way. 

Errors from log file : 

"Undefined subroutine &JSON::from_json called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 766."
"Premature end of script headers: gbrowse"

Does they mean, am i missing any libraries or required files for subtrack in gbrowse? my gbrowse version is 2.23. will that have any effect?  


while troubleshooting, i am emptying cache from browser everytime as well.. 




On Wed, Sep 18, 2013 at 3:28 PM, Timothy Parnell <[hidden email]> wrote:
Try taking out the bump and opacity options. I don't think the transparency overlap works with the wiggle_density glyph. I know it does not work with wiggle_whiskers, but works perfectly well with wiggle_xyplot.

Also, as a reminder, when troubleshooting, make sure to navigate to different coordinates to avoid cache issues.


On Sep 18, 2013, at 11:54 AM, Timothy Parnell <[hidden email]> wrote:

> Ah, my mistake.
>
> The subtrack select requires two values, delimited by space, a human-interpretable label and then the feature method. So, it should be, for example,
>
> subtrack select = Sample method
>
> Tim
>
> On Sep 18, 2013, at 11:20 AM, empyrean999 <[hidden email]<mailto:[hidden email]>>
> wrote:
>
>
> Thank you for your prompt response, Tim.
>
> I did changed feature to summary, subtract select = method and i am using bigwigset adaptor. After modifying them, my conf and meta data files looks like this.
>
> [soy_test:database]
> db_adaptor    = Bio::DB::BigWigSet
> db_args       = -dir /home/soybean/bigwig
> search options = none
>
>
> [soy_atlas_test]
> feature  = summary
> category = Test
> database = soy_atlas_test
> glyph    = wiggle_density
> height = 30
> bicolor_pivot = 20
> pos_color = blue
> neg_color = red
> key       = soyatlas read density
> bump  = overlap
> opacity = 0.5
> subtrack select  = method
> subtrack table   = Sample_3 *;
>                   Sample_4 *;
>                   Sample_5 *;
>
> ###meta data####
>
> [Sample_3.bw]
> display_name = "root"
> method       = Sample_3
>
> [Sample_4.bw]
> display_name = "shoot"
> method       = Sample_4
>
> [Sample_5.bw]
> display_name = "seed"
> method       = Sample_5
>
>
> But i am getting some error at track " Track Rendering error : Not a code reference at (eval 116) line 6 " Attached the figure below..
>
> When i looked at error log file, i see the following things.
>
> Use of uninitialized value in string eq at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 322
> Use of uninitialized value in concatenation (.) or string at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 326.
> Use of uninitialized value in string eq at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 315.
> Use of uninitialized value in string eq at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 322.,
> Use of uninitialized value in concatenation (.) or string at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 326., referer:
> Use of uninitialized value in exists at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2.pm line 395.
>
>
> Thanks again for your support and help !
>
>
>
> On Wed, Sep 18, 2013 at 12:41 PM, Timothy Parnell <[hidden email]<mailto:[hidden email]>> wrote:
> Hi,
>
> I see a couple of things.
>
> First, you have a duplicate feature line in the conf stanza, which means it will use the last one. You should just use the summary feature (the coverage feature won't be recognized by the database adaptor). By the way, you are using the Bio::DB::BigWigSet adaptor, right?
>
> Second, the subtrack select needs to have a valid method or attribute to filter. The metadata file does not list a tissue attribute. But since you have both "display_name" and "method" attributes, you can simply use those for your selection. So set
> subtrack select = method
>
> I think that will work.
>
> Tim
>
> On Sep 18, 2013, at 10:07 AM, empyrean999 <[hidden email]<mailto:[hidden email]>> wrote:
>
>> Hi.. i have Mapping data for 3 different tissues. I mapped to soybean genome. I converted bam to bedgraph to bigwig. Now i have bigwig files for 3 tissues. i am trying to upload to gbrowse using subtracks. I can see the subtracks track and popup but no data is pulling from  my metadata file.
>>
>> please correct me where i am doing wrong.
>>
>> I have attached a screenshot from soybase showing subtracks of transcript density for different tissues. i need to get my bigwigs in to similar format.
>>
>> ###Conf file #####
>>
>> [soy_test]
>> feature  = summary
>> category = Reads
>> feature  = coverage
>> database = soy_atlas_test
>> glyph    = wiggle_density
>> height = 30
>> bicolor_pivot = 20
>> pos_color = blue
>> neg_color = red
>> key       = soyatlas read density
>> bump  = overlap
>> opacity = 0.5
>> subtrack select  = Tissue tag_value tissue
>> subtrack table   = Sample_3 *;
>>                   Sample_4 *;
>>                   Sample_5 *;
>> scale = both
>>
>> ###metafile####
>> [Sample_3.bw]
>> display_name = "Leaf"
>> method       = Sample_3
>>
>> [Sample_4.bw]
>> display_name = "Root"
>> method       = Sample_4
>>
>> [Sample_5.bw]
>> display_name = "Seed"
>> method       = Sample_5
>>
>>
>>
>>
>> <soybase_subtracks.PNG>------------------------------------------------------------------------------
>> LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99!
>> 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint
>> 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes
>> Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13.
>> http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk_______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]<mailto:[hidden email]>
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
> <soy_error.PNG>------------------------------------------------------------------------------
> LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99!
> 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint
> 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes
> Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13.
> http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk_______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
> ------------------------------------------------------------------------------
> LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99!
> 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint
> 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes
> Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13.
> http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk
> _______________________________________________
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2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes
Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13.
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--
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: GBrowse Subtracks

empyrean
thanks for the info scott.

I will look in to JSON module and try to update it. Coming to updating gbrowse, i dont know how easily it can be done. Gbrowse is hosted on a seperate server internally and connected to several groups. I am looking after this for couple of months. The admin who used to take care of gbrowse suggested not to upgrade since he has many scripts tied in to it and that might break thinks all together ! so i am skeptical on doing that !!


On Wed, Sep 18, 2013 at 4:20 PM, Scott Cain <[hidden email]> wrote:
Hi,

The undefined subroutine may indicate that, while you might have the JSON module installed, it might be old so that the version you have might not have the from_json method, or JSON isn't installed at all; either way, check into updating it.

Additionally, 2.23 is a really old version of GBrowse, which will make troubleshooting it really difficult.  Would it be possible to upgrade to something newer?

Scott



On Wed, Sep 18, 2013 at 4:02 PM, empyrean999 <[hidden email]> wrote:
I took those options. Before that, i tried changing from wiggle_density to wiggle_xyplot also.. no change.. when deselect subtracks and clicked "change" it seems to load but still blank track but the when i open the subtracks popup again, they seem to select by themselves. I removed * after subtrack table also still behaving the same way. 

Errors from log file : 

"Undefined subroutine &JSON::from_json called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 766."
"Premature end of script headers: gbrowse"

Does they mean, am i missing any libraries or required files for subtrack in gbrowse? my gbrowse version is 2.23. will that have any effect?  


while troubleshooting, i am emptying cache from browser everytime as well.. 




On Wed, Sep 18, 2013 at 3:28 PM, Timothy Parnell <[hidden email]> wrote:
Try taking out the bump and opacity options. I don't think the transparency overlap works with the wiggle_density glyph. I know it does not work with wiggle_whiskers, but works perfectly well with wiggle_xyplot.

Also, as a reminder, when troubleshooting, make sure to navigate to different coordinates to avoid cache issues.


On Sep 18, 2013, at 11:54 AM, Timothy Parnell <[hidden email]> wrote:

> Ah, my mistake.
>
> The subtrack select requires two values, delimited by space, a human-interpretable label and then the feature method. So, it should be, for example,
>
> subtrack select = Sample method
>
> Tim
>
> On Sep 18, 2013, at 11:20 AM, empyrean999 <[hidden email]<mailto:[hidden email]>>
> wrote:
>
>
> Thank you for your prompt response, Tim.
>
> I did changed feature to summary, subtract select = method and i am using bigwigset adaptor. After modifying them, my conf and meta data files looks like this.
>
> [soy_test:database]
> db_adaptor    = Bio::DB::BigWigSet
> db_args       = -dir /home/soybean/bigwig
> search options = none
>
>
> [soy_atlas_test]
> feature  = summary
> category = Test
> database = soy_atlas_test
> glyph    = wiggle_density
> height = 30
> bicolor_pivot = 20
> pos_color = blue
> neg_color = red
> key       = soyatlas read density
> bump  = overlap
> opacity = 0.5
> subtrack select  = method
> subtrack table   = Sample_3 *;
>                   Sample_4 *;
>                   Sample_5 *;
>
> ###meta data####
>
> [Sample_3.bw]
> display_name = "root"
> method       = Sample_3
>
> [Sample_4.bw]
> display_name = "shoot"
> method       = Sample_4
>
> [Sample_5.bw]
> display_name = "seed"
> method       = Sample_5
>
>
> But i am getting some error at track " Track Rendering error : Not a code reference at (eval 116) line 6 " Attached the figure below..
>
> When i looked at error log file, i see the following things.
>
> Use of uninitialized value in string eq at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 322
> Use of uninitialized value in concatenation (.) or string at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 326.
> Use of uninitialized value in string eq at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 315.
> Use of uninitialized value in string eq at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 322.,
> Use of uninitialized value in concatenation (.) or string at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SubtrackTable.pm line 326., referer:
> Use of uninitialized value in exists at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2.pm line 395.
>
>
> Thanks again for your support and help !
>
>
>
> On Wed, Sep 18, 2013 at 12:41 PM, Timothy Parnell <[hidden email]<mailto:[hidden email]>> wrote:
> Hi,
>
> I see a couple of things.
>
> First, you have a duplicate feature line in the conf stanza, which means it will use the last one. You should just use the summary feature (the coverage feature won't be recognized by the database adaptor). By the way, you are using the Bio::DB::BigWigSet adaptor, right?
>
> Second, the subtrack select needs to have a valid method or attribute to filter. The metadata file does not list a tissue attribute. But since you have both "display_name" and "method" attributes, you can simply use those for your selection. So set
> subtrack select = method
>
> I think that will work.
>
> Tim
>
> On Sep 18, 2013, at 10:07 AM, empyrean999 <[hidden email]<mailto:[hidden email]>> wrote:
>
>> Hi.. i have Mapping data for 3 different tissues. I mapped to soybean genome. I converted bam to bedgraph to bigwig. Now i have bigwig files for 3 tissues. i am trying to upload to gbrowse using subtracks. I can see the subtracks track and popup but no data is pulling from  my metadata file.
>>
>> please correct me where i am doing wrong.
>>
>> I have attached a screenshot from soybase showing subtracks of transcript density for different tissues. i need to get my bigwigs in to similar format.
>>
>> ###Conf file #####
>>
>> [soy_test]
>> feature  = summary
>> category = Reads
>> feature  = coverage
>> database = soy_atlas_test
>> glyph    = wiggle_density
>> height = 30
>> bicolor_pivot = 20
>> pos_color = blue
>> neg_color = red
>> key       = soyatlas read density
>> bump  = overlap
>> opacity = 0.5
>> subtrack select  = Tissue tag_value tissue
>> subtrack table   = Sample_3 *;
>>                   Sample_4 *;
>>                   Sample_5 *;
>> scale = both
>>
>> ###metafile####
>> [Sample_3.bw]
>> display_name = "Leaf"
>> method       = Sample_3
>>
>> [Sample_4.bw]
>> display_name = "Root"
>> method       = Sample_4
>>
>> [Sample_5.bw]
>> display_name = "Seed"
>> method       = Sample_5
>>
>>
>>
>>
>> <soybase_subtracks.PNG>------------------------------------------------------------------------------
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>
>
> <soy_error.PNG>------------------------------------------------------------------------------
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--
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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