Adding new data

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Adding new data

Nitish Narula
Hello,

I have more genomic data to add to the GBrowse page. Given the GFF3 file of this new data, I am planning to use the bp_fast_load_gff.pl to add the new data to the database. Here is the General section of the configuration file:

[GENERAL]
description   = Cryphonectria parasitica v.2 reads mapped to the reference genome
db_adaptor    = Bio::DB::GFF
db_args       = -adaptor dbi::mysql
        -dsn     dbi:mysql:database=CParasitica_NT_N_v2;host=xxx.xxx.xx.xxx;user=nobody;pass=

We want the new data to be displayed as a separate track. How would I go about editing the .conf file to allow that? 

I am a beginner at GBrowse and databases. I may not be providing enough information for this question to be answered but I do not know what information I need to provide. Please let me know what I can do to help you help me. 

Thank you so much!

Nitish Narula

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Cloud computing makes use of virtualization - but cloud computing
also focuses on allowing computing to be delivered as a service.
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Re: Adding new data

Jayaraman, Pushkala

Since you’re using GFF and bp_load_gff.pl, This should help you out..

http://gmod.org/wiki/GBrowse_1_Configuration_HOWTO

 

If you guys ever move to bio::db::seqfeature::store, i.e GBrowse2, this should help you:

http://gmod.org/wiki/GBrowse_2.0_HOWTO#Data_Source_Configuration_Files

 

Pushkala Jayaraman

Programmer/Analyst - Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

414-955-2229

http://rgd.mcw.edu

 

From: Nitish Narula [mailto:[hidden email]]
Sent: Wednesday, February 08, 2012 4:25 PM
To: [hidden email]
Subject: [Gmod-gbrowse] Adding new data

 

Hello,

 

I have more genomic data to add to the GBrowse page. Given the GFF3 file of this new data, I am planning to use the bp_fast_load_gff.pl to add the new data to the database. Here is the General section of the configuration file:

 

[GENERAL]

description   = Cryphonectria parasitica v.2 reads mapped to the reference genome

db_adaptor    = Bio::DB::GFF

db_args       = -adaptor dbi::mysql

        -dsn     dbi:mysql:database=CParasitica_NT_N_v2;host=xxx.xxx.xx.xxx;user=nobody;pass=

 

We want the new data to be displayed as a separate track. How would I go about editing the .conf file to allow that? 

 

I am a beginner at GBrowse and databases. I may not be providing enough information for this question to be answered but I do not know what information I need to provide. Please let me know what I can do to help you help me. 

 

Thank you so much!

 

Nitish Narula


------------------------------------------------------------------------------
Virtualization & Cloud Management Using Capacity Planning
Cloud computing makes use of virtualization - but cloud computing
also focuses on allowing computing to be delivered as a service.
http://www.accelacomm.com/jaw/sfnl/114/51521223/
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Re: Adding new data

Todd Harris
Bio::DB::SeqFeature is tied to GFF3.  GBrowse2 has no preference over GFF2 or GFF3.

th


On Feb 9, 2012, at 9:44 AM, "Jayaraman, Pushkala" <[hidden email]> wrote:

Since you’re using GFF and bp_load_gff.pl, This should help you out..

http://gmod.org/wiki/GBrowse_1_Configuration_HOWTO

 

If you guys ever move to bio::db::seqfeature::store, i.e GBrowse2, this should help you:

http://gmod.org/wiki/GBrowse_2.0_HOWTO#Data_Source_Configuration_Files

 

Pushkala Jayaraman

Programmer/Analyst - Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

414-955-2229

http://rgd.mcw.edu

 

From: Nitish Narula [mailto:[hidden email]]
Sent: Wednesday, February 08, 2012 4:25 PM
To: [hidden email]
Subject: [Gmod-gbrowse] Adding new data

 

Hello,

 

I have more genomic data to add to the GBrowse page. Given the GFF3 file of this new data, I am planning to use the bp_fast_load_gff.pl to add the new data to the database. Here is the General section of the configuration file:

 

[GENERAL]

description   = Cryphonectria parasitica v.2 reads mapped to the reference genome

db_adaptor    = Bio::DB::GFF

db_args       = -adaptor dbi::mysql

        -dsn     dbi:mysql:database=CParasitica_NT_N_v2;host=xxx.xxx.xx.xxx;user=nobody;pass=

 

We want the new data to be displayed as a separate track. How would I go about editing the .conf file to allow that? 

 

I am a beginner at GBrowse and databases. I may not be providing enough information for this question to be answered but I do not know what information I need to provide. Please let me know what I can do to help you help me. 

 

Thank you so much!

 

Nitish Narula

------------------------------------------------------------------------------
Virtualization & Cloud Management Using Capacity Planning
Cloud computing makes use of virtualization - but cloud computing
also focuses on allowing computing to be delivered as a service.
http://www.accelacomm.com/jaw/sfnl/114/51521223/
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

------------------------------------------------------------------------------
Virtualization & Cloud Management Using Capacity Planning
Cloud computing makes use of virtualization - but cloud computing
also focuses on allowing computing to be delivered as a service.
http://www.accelacomm.com/jaw/sfnl/114/51521223/
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
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