FW: [Gmod-gbrowse] help with wiggle track display

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FW: [Gmod-gbrowse] help with wiggle track display

Jayaraman, Pushkala

Hello,

I need help with this track.. I am not able to get it to show up on Gbrowse.. and Im not sure what I need to change..

Hoping to get some idea.. J

 

 

Hello,

I know there are multiple posts about problems with individual wiggle track displays.. but I seem to be stuck in this as well..

I have the Conservation Score files from UCSC and I am trying to upload them on Gbrowse.

 

The files look like this..

As you can see, not all positions have scores. Hence there are multiple places in the same file that have the “fixedStep chrom=Chr18 start=XXXXXX step=1”

 

fixedStep chrom=Chr18 start=28760 step=1

0.000

0.000

0.000

0.001

0.000

0.000

0.000

0.000

0.000

0.000

0.000

0.001

0.001

0.003

0.010

0.015

0.020

0.023

0.026

0.028

0.029

0.029

0.030

0.029

fixedStep chrom=Chr18 start=31859 step=1

0.073

0.103

0.151

0.182

0.256

0.375

0.571

0.656

0.712

0.841

0.894

0.929

0.943

0.953

0.969

0.981

0.986

0.988

0.989

0.988

0.986

0.980

0.971

0.966

0.954

0.936

….

 

 

So I added the line only at the head of each file(irrespective of how many times it has the line fixedStep chrom=Chr18… repeated):

track type=wiggle_0 name="fixedStep" description="fixedStep format" visibility=full autoScale=off viewLimits=0:1000 color=0,200,100

 

and then ran the wiggle2gff2.pl script.

I get this line in the gff3 file:

##gff-version 3

 

Chr18   rgd     Conservation    28760   87247357        .       .       .       Name=fixedStep;Note=fixedStep%20format;wigfile=/rgd/gbrowse2/databases/Conscore/track_001.Chr18.1293125672.wib

 

 

 

I use the bp_seqfeature_load.pl script to load these files into the DB. But then I get a blank track(first wiggle file). No errors either.

Where am I going wrong?

 

Am I supposed to add the line: “track type=wiggle_0 name="fixedStep" description="fixedStep format" visibility=full autoScale=off viewLimits=0:1000 color=0,200,100“ each time the line fixedStep chrom=Chr18.. repeats itself in the file?

 

Here is the image:

 

 

And here is the configuration :

[TEST_WIG]

feature = Conservation

glyph   = wiggle_xyplot

key     = first wiggle file

category = DETAILS:Annotated Variants

 

 

Thanks,

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 


------------------------------------------------------------------------------
Learn how Oracle Real Application Clusters (RAC) One Node allows customers
to consolidate database storage, standardize their database environment, and,
should the need arise, upgrade to a full multi-node Oracle RAC database
without downtime or disruption
http://p.sf.net/sfu/oracle-sfdevnl
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Re: FW: [Gmod-gbrowse] help with wiggle track display

Scott Cain
Hi Pushkala,

I'm not sure the GBrowse wiggle converter script supports multiple "fixedStep" lines in a single wiggle file.  I've never seen that in a wiggle file before (though I admittedly have limited experience with them).  If you trim those out but otherwise leave the file the same, does it work (though no doubt with screwed up coordinates)?  Perhaps you'll need to split these into separate files.

Scott


On Tue, Dec 28, 2010 at 11:14 AM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello,

I need help with this track.. I am not able to get it to show up on Gbrowse.. and Im not sure what I need to change..

Hoping to get some idea.. J

 

 

Hello,

I know there are multiple posts about problems with individual wiggle track displays.. but I seem to be stuck in this as well..

I have the Conservation Score files from UCSC and I am trying to upload them on Gbrowse.

 

The files look like this..

As you can see, not all positions have scores. Hence there are multiple places in the same file that have the “fixedStep chrom=Chr18 start=XXXXXX step=1”

 

fixedStep chrom=Chr18 start=28760 step=1

0.000

0.000

0.000

0.001

0.000

0.000

0.000

0.000

0.000

0.000

0.000

0.001

0.001

0.003

0.010

0.015

0.020

0.023

0.026

0.028

0.029

0.029

0.030

0.029

fixedStep chrom=Chr18 start=31859 step=1

0.073

0.103

0.151

0.182

0.256

0.375

0.571

0.656

0.712

0.841

0.894

0.929

0.943

0.953

0.969

0.981

0.986

0.988

0.989

0.988

0.986

0.980

0.971

0.966

0.954

0.936

….

 

 

So I added the line only at the head of each file(irrespective of how many times it has the line fixedStep chrom=Chr18… repeated):

track type=wiggle_0 name="fixedStep" description="fixedStep format" visibility=full autoScale=off viewLimits=0:1000 color=0,200,100

 

and then ran the wiggle2gff2.pl script.

I get this line in the gff3 file:

##gff-version 3

 

Chr18   rgd     Conservation    28760   87247357        .       .       .       Name=fixedStep;Note=fixedStep%20format;wigfile=/rgd/gbrowse2/databases/Conscore/track_001.Chr18.1293125672.wib

 

 

 

I use the bp_seqfeature_load.pl script to load these files into the DB. But then I get a blank track(first wiggle file). No errors either.

Where am I going wrong?

 

Am I supposed to add the line: “track type=wiggle_0 name="fixedStep" description="fixedStep format" visibility=full autoScale=off viewLimits=0:1000 color=0,200,100“ each time the line fixedStep chrom=Chr18.. repeats itself in the file?

 

Here is the image:

 

 

And here is the configuration :

[TEST_WIG]

feature = Conservation

glyph   = wiggle_xyplot

key     = first wiggle file

category = DETAILS:Annotated Variants

 

 

Thanks,

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 


------------------------------------------------------------------------------
Learn how Oracle Real Application Clusters (RAC) One Node allows customers
to consolidate database storage, standardize their database environment, and,
should the need arise, upgrade to a full multi-node Oracle RAC database
without downtime or disruption
http://p.sf.net/sfu/oracle-sfdevnl
_______________________________________________
Gmod-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-devel




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Learn how Oracle Real Application Clusters (RAC) One Node allows customers
to consolidate database storage, standardize their database environment, and,
should the need arise, upgrade to a full multi-node Oracle RAC database
without downtime or disruption
http://p.sf.net/sfu/oracle-sfdevnl
_______________________________________________
Gmod-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-devel
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Re: FW: [Gmod-gbrowse] help with wiggle track display

Jayaraman, Pushkala

Thanks Scott,

Ill try this.. there isn’t just two “fixedStep headings..

Each chromosome file has atleast 10-20 of those headings..

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, December 28, 2010 11:02 AM
To: Jayaraman, Pushkala
Cc: gbrowse List; [hidden email]
Subject: Re: [GMOD-devel] FW: [Gmod-gbrowse] help with wiggle track display

 

Hi Pushkala,

I'm not sure the GBrowse wiggle converter script supports multiple "fixedStep" lines in a single wiggle file.  I've never seen that in a wiggle file before (though I admittedly have limited experience with them).  If you trim those out but otherwise leave the file the same, does it work (though no doubt with screwed up coordinates)?  Perhaps you'll need to split these into separate files.

Scott

On Tue, Dec 28, 2010 at 11:14 AM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello,

I need help with this track.. I am not able to get it to show up on Gbrowse.. and Im not sure what I need to change..

Hoping to get some idea.. J

 

 

Hello,

I know there are multiple posts about problems with individual wiggle track displays.. but I seem to be stuck in this as well..

I have the Conservation Score files from UCSC and I am trying to upload them on Gbrowse.

 

The files look like this..

As you can see, not all positions have scores. Hence there are multiple places in the same file that have the “fixedStep chrom=Chr18 start=XXXXXX step=1”

 

fixedStep chrom=Chr18 start=28760 step=1

0.000

0.000

0.000

0.001

0.000

0.000

0.000

0.000

0.000

0.000

0.000

0.001

0.001

0.003

0.010

0.015

0.020

0.023

0.026

0.028

0.029

0.029

0.030

0.029

fixedStep chrom=Chr18 start=31859 step=1

0.073

0.103

0.151

0.182

0.256

0.375

0.571

0.656

0.712

0.841

0.894

0.929

0.943

0.953

0.969

0.981

0.986

0.988

0.989

0.988

0.986

0.980

0.971

0.966

0.954

0.936

….

 

 

So I added the line only at the head of each file(irrespective of how many times it has the line fixedStep chrom=Chr18… repeated):

track type=wiggle_0 name="fixedStep" description="fixedStep format" visibility=full autoScale=off viewLimits=0:1000 color=0,200,100

 

and then ran the wiggle2gff2.pl script.

I get this line in the gff3 file:

##gff-version 3

 

Chr18   rgd     Conservation    28760   87247357        .       .       .       Name=fixedStep;Note=fixedStep%20format;wigfile=/rgd/gbrowse2/databases/Conscore/track_001.Chr18.1293125672.wib

 

 

 

I use the bp_seqfeature_load.pl script to load these files into the DB. But then I get a blank track(first wiggle file). No errors either.

Where am I going wrong?

 

Am I supposed to add the line: “track type=wiggle_0 name="fixedStep" description="fixedStep format" visibility=full autoScale=off viewLimits=0:1000 color=0,200,100“ each time the line fixedStep chrom=Chr18.. repeats itself in the file?

 

Here is the image:

 

 

And here is the configuration :

[TEST_WIG]

feature = Conservation

glyph   = wiggle_xyplot

key     = first wiggle file

category = DETAILS:Annotated Variants

 

 

Thanks,

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 


------------------------------------------------------------------------------
Learn how Oracle Real Application Clusters (RAC) One Node allows customers
to consolidate database storage, standardize their database environment, and,
should the need arise, upgrade to a full multi-node Oracle RAC database
without downtime or disruption
http://p.sf.net/sfu/oracle-sfdevnl
_______________________________________________
Gmod-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-devel




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
Learn how Oracle Real Application Clusters (RAC) One Node allows customers
to consolidate database storage, standardize their database environment, and,
should the need arise, upgrade to a full multi-node Oracle RAC database
without downtime or disruption
http://p.sf.net/sfu/oracle-sfdevnl
_______________________________________________
Gmod-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-devel