[Gmod-ajax] Problem with high number of Contigs in Jbrowse

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[Gmod-ajax] Problem with high number of Contigs in Jbrowse

Seyed Ahmad Mousavi
Hi

Firstly, I should say that I'm a new Jbrowse user and I have a draft genome sequences that consists near 30.000 contig sequences.  I would like to use JBrowse for visualizing them. But Jbrowse shows just first 30 sequences and I don't have access to other ones. 

Enclosed image shows my output for draft genome.

I have 3 question, that I appreciate if you reply:


1- How can I increase the number of sequences in drop down list from 30 to more than 30?

2- Is it normal to use JBrowse or GMOD for visualization of these high number of sequences?

3- What approach you recommend to me for showing this draft genome via JBrowse, Can I concatenate them into 1 sequence file, If yes please tell me how?

Kind regards,
--
Ahmad


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Re: Problem with high number of Contigs in Jbrowse

Hans Vasquez-Gross
Hi Ahmad,

I have worked with JBrowse for some time and can help with your questions.

1) I'm not sure if you can increase the dropdown list.  However, if you run generate-names.pl, you can have the text search box on to the right autocomplete names as you type the contig name.  That's what I do for my database.

2) Yes, I run JBrowse for displaying the wheat reference which is still an early release. It has 10,302,538 contigs which are organized by chromosome arm into sub datasets.  

3) If you have your contigs somehow sorted into logical chunks (IE for my reference by chromosome arm), then you can host these chunks into datasets.  You can search the jbrowse list for some help emails when I was first setting this up.  Here is one such post: http://gmod.827538.n3.nabble.com/Gmod-ajax-Multiple-Datasets-configuration-td4040943.html

Cheers,
-Hans

On Wed, Jul 13, 2016 at 2:46 AM, Seyed Ahmad Mousavi <[hidden email]> wrote:
Hi

Firstly, I should say that I'm a new Jbrowse user and I have a draft genome sequences that consists near 30.000 contig sequences.  I would like to use JBrowse for visualizing them. But Jbrowse shows just first 30 sequences and I don't have access to other ones. 

Enclosed image shows my output for draft genome.

I have 3 question, that I appreciate if you reply:


1- How can I increase the number of sequences in drop down list from 30 to more than 30?

2- Is it normal to use JBrowse or GMOD for visualization of these high number of sequences?

3- What approach you recommend to me for showing this draft genome via JBrowse, Can I concatenate them into 1 sequence file, If yes please tell me how?

Kind regards,
--
Ahmad


------------------------------------------------------------------------------
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patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
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--
Hans Vasquez-Gross
Graduate Student
Department of Plant Science
University of California at Davis
Skype: hansvg.ucd

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patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
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Re: Problem with high number of Contigs in Jbrowse

Keiran Raine
Hi,

You can configure the max size of the drop down as described here:


However as Hans indicates making your contigs searchable is probably more use with this number.

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

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

On 13 Jul 2016, at 23:01, Hans Vasquez-Gross <[hidden email]> wrote:

Hi Ahmad,

I have worked with JBrowse for some time and can help with your questions.

1) I'm not sure if you can increase the dropdown list.  However, if you run generate-names.pl, you can have the text search box on to the right autocomplete names as you type the contig name.  That's what I do for my database.

2) Yes, I run JBrowse for displaying the wheat reference which is still an early release. It has 10,302,538 contigs which are organized by chromosome arm into sub datasets.  

3) If you have your contigs somehow sorted into logical chunks (IE for my reference by chromosome arm), then you can host these chunks into datasets.  You can search the jbrowse list for some help emails when I was first setting this up.  Here is one such post: http://gmod.827538.n3.nabble.com/Gmod-ajax-Multiple-Datasets-configuration-td4040943.html

Cheers,
-Hans

On Wed, Jul 13, 2016 at 2:46 AM, Seyed Ahmad Mousavi <[hidden email]> wrote:
Hi

Firstly, I should say that I'm a new Jbrowse user and I have a draft genome sequences that consists near 30.000 contig sequences.  I would like to use JBrowse for visualizing them. But Jbrowse shows just first 30 sequences and I don't have access to other ones. 

Enclosed image shows my output for draft genome.

I have 3 question, that I appreciate if you reply:


1- How can I increase the number of sequences in drop down list from 30 to more than 30?

2- Is it normal to use JBrowse or GMOD for visualization of these high number of sequences?

3- What approach you recommend to me for showing this draft genome via JBrowse, Can I concatenate them into 1 sequence file, If yes please tell me how?

Kind regards,
--
Ahmad


------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
_______________________________________________
Gmod-ajax mailing list
[hidden email]
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--
Hans Vasquez-Gross
Graduate Student
Department of Plant Science
University of California at Davis
Skype: hansvg.ucd
------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev_______________________________________________
Gmod-ajax mailing list
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-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
_______________________________________________
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Re: Problem with high number of Contigs in Jbrowse

Seyed Ahmad Mousavi
In reply to this post by Hans Vasquez-Gross
Hi Hans,

Thank you so much for help.


 I run  generate-names.pl without parameter, which still running on my server. I hope it could help me to search gene name through search box.

It would be hopeful to hear you run Jbrowse for wheat contigs. Actually, our genome sequencing project is on the beginning and we have just contigs due to its huge number of redundant sequences.

I think it is enough for users to search gene names or transcript IDs or other available features at GFF files, which you mentioned it is possible.

Thanks.
Ahmad




On Thu, Jul 14, 2016 at 2:31 AM, Hans Vasquez-Gross <[hidden email]> wrote:
Hi Ahmad,

I have worked with JBrowse for some time and can help with your questions.

1) I'm not sure if you can increase the dropdown list.  However, if you run generate-names.pl, you can have the text search box on to the right autocomplete names as you type the contig name.  That's what I do for my database.

2) Yes, I run JBrowse for displaying the wheat reference which is still an early release. It has 10,302,538 contigs which are organized by chromosome arm into sub datasets.  

3) If you have your contigs somehow sorted into logical chunks (IE for my reference by chromosome arm), then you can host these chunks into datasets.  You can search the jbrowse list for some help emails when I was first setting this up.  Here is one such post: http://gmod.827538.n3.nabble.com/Gmod-ajax-Multiple-Datasets-configuration-td4040943.html

Cheers,
-Hans

On Wed, Jul 13, 2016 at 2:46 AM, Seyed Ahmad Mousavi <[hidden email]> wrote:
Hi

Firstly, I should say that I'm a new Jbrowse user and I have a draft genome sequences that consists near 30.000 contig sequences.  I would like to use JBrowse for visualizing them. But Jbrowse shows just first 30 sequences and I don't have access to other ones. 

Enclosed image shows my output for draft genome.

I have 3 question, that I appreciate if you reply:


1- How can I increase the number of sequences in drop down list from 30 to more than 30?

2- Is it normal to use JBrowse or GMOD for visualization of these high number of sequences?

3- What approach you recommend to me for showing this draft genome via JBrowse, Can I concatenate them into 1 sequence file, If yes please tell me how?

Kind regards,
--
Ahmad


------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




--
Hans Vasquez-Gross
Graduate Student
Department of Plant Science
University of California at Davis
Skype: hansvg.ucd


------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
_______________________________________________
Gmod-ajax mailing list
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