Re: info on Jbrowse

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Re: info on Jbrowse

Scott Cain
Hi Luca,

I'm cc'ing the JBrowse mailing list so people there can chime in too.

With JBrowse, you can visualize anything you want; all you need are coordinates of the features on the sequence you want to see (regardless of whether the sequence is "real" or not as you've suggested).  The only thing that you might want to do that JBrowse can't do is automatically map between different levels of assembly.  For example, if you have genes on contigs and the contigs mapped in to a scaffold, JBrowse can't automatically display the genes on the scaffold (but you can create a GFF file where you map the genes onto the scaffold).

There's no reason you can't show multiple levels of sequences in the same instance of JBrowse (contigs, scaffolds and LGs).  It would take some configuration to make clicking on contigs as they appear in a scaffold to take take you to that contig's JBrowse display, but it would not be terribly hard.  I suspect the hardest aspect of setting this JBrowse instance up will be getting the source data looking the way you want before you import it into JBrowse.

Please let us know if you have more questions.

Scott


On Fri, Apr 22, 2016 at 7:00 AM, Luca Bianco <[hidden email]> wrote:
Hello,

We are trying to use Jbrowse to visualize the information on the apple genome (Malus x Domestica) but we are hitting some problems. The genome is a high quality improved draft genome, which is heterozygous.

The current structure of the genome is organized as follows:
17 linkage groups  made by a number of scaffolds made by a number of contigs. We do not have the consensus sequence of scaffolds but only the approximate position (obtained through genetic markers) of contigs within scaffolds and that of scaffolds within LGs. 

Some scaffolds overlap some others and the same applies to contigs.

The problem we are facing is the fact that all the features refer to a refSeq (from you reference: "The reference sequences on which the browser will display annotations, and which provide a common coordinate system for all tracks"). 

If we understand the software correctly, the only sequence we are sure of is that of contigs but we would like to browse the genome LG by LG with the possibility of visualizing the scaffolding information down to the level of the contig for which we would like to access also sequence data. 

We are unsure on how to set this up on Jbrowse as if we specify the sequence of contigs then we have the correct information on the sequence but miss the higher level structures of scaffolds and LGs.
On the contrary, specifying LG level sequence would be highly imprecise and we would not be able to retrieve the correct contig sequence  in overlapping genomes.

Is it possible to specify a "fake" reference sequence (something like a string of Ns), but enabling the visualization of contig sequence when clicking on the contigs track?

Thanks for your help. Best Wishes,
Luca
  
--
Luca Bianco, Ph.D.
tel +39-0461615134
Computational Biology Department
FEM Research and Innovation Center
Via E. Mach,1
38010 San Michele all'Adige (TN)
Italy



--
------------------------------------------------------------------------
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: info on Jbrowse

Suzanna Lewis-3
Actually virtual ref. sequences (computational ligation, contig stapling, etc.) is something we (i.e. Nathan Dunn) are just about to roll out soon in Apollo. It enables the curator to 'manually assemble' the contigs (correct order and orientation) to create a virtual ref. sequence.

I'll let either Moni or Nathan provide more details and an ETA for this imminent release

-S


On Fri, Apr 22, 2016 at 6:51 AM, Scott Cain <[hidden email]> wrote:
Hi Luca,

I'm cc'ing the JBrowse mailing list so people there can chime in too.

With JBrowse, you can visualize anything you want; all you need are coordinates of the features on the sequence you want to see (regardless of whether the sequence is "real" or not as you've suggested).  The only thing that you might want to do that JBrowse can't do is automatically map between different levels of assembly.  For example, if you have genes on contigs and the contigs mapped in to a scaffold, JBrowse can't automatically display the genes on the scaffold (but you can create a GFF file where you map the genes onto the scaffold).

There's no reason you can't show multiple levels of sequences in the same instance of JBrowse (contigs, scaffolds and LGs).  It would take some configuration to make clicking on contigs as they appear in a scaffold to take take you to that contig's JBrowse display, but it would not be terribly hard.  I suspect the hardest aspect of setting this JBrowse instance up will be getting the source data looking the way you want before you import it into JBrowse.

Please let us know if you have more questions.

Scott


On Fri, Apr 22, 2016 at 7:00 AM, Luca Bianco <[hidden email]> wrote:
Hello,

We are trying to use Jbrowse to visualize the information on the apple genome (Malus x Domestica) but we are hitting some problems. The genome is a high quality improved draft genome, which is heterozygous.

The current structure of the genome is organized as follows:
17 linkage groups  made by a number of scaffolds made by a number of contigs. We do not have the consensus sequence of scaffolds but only the approximate position (obtained through genetic markers) of contigs within scaffolds and that of scaffolds within LGs. 

Some scaffolds overlap some others and the same applies to contigs.

The problem we are facing is the fact that all the features refer to a refSeq (from you reference: "The reference sequences on which the browser will display annotations, and which provide a common coordinate system for all tracks"). 

If we understand the software correctly, the only sequence we are sure of is that of contigs but we would like to browse the genome LG by LG with the possibility of visualizing the scaffolding information down to the level of the contig for which we would like to access also sequence data. 

We are unsure on how to set this up on Jbrowse as if we specify the sequence of contigs then we have the correct information on the sequence but miss the higher level structures of scaffolds and LGs.
On the contrary, specifying LG level sequence would be highly imprecise and we would not be able to retrieve the correct contig sequence  in overlapping genomes.

Is it possible to specify a "fake" reference sequence (something like a string of Ns), but enabling the visualization of contig sequence when clicking on the contigs track?

Thanks for your help. Best Wishes,
Luca
  
--
Luca Bianco, Ph.D.
tel +39-0461615134
Computational Biology Department
FEM Research and Innovation Center
Via E. Mach,1
38010 San Michele all'Adige (TN)
Italy



--
------------------------------------------------------------------------
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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Re: info on Jbrowse

nathandunn

Luca / Scott,

What we trying to put together with Apollo is the ability to virtually connect and browse scaffolds (sorry the graphics are still VERY a work in progress, but the data is real):


This includes the ability to put together arbitrary gene regions as well:


One of the main goals (there are many) is to allow user’s to create genomic annotations across these regions. 

I’m hoping to have a working beta in the next month or so with a release this summer (with a much improved interface).   

Let us know if you have any questions.  

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On Apr 26, 2016, at 4:37 PM, Suzanna Lewis <[hidden email]> wrote:

Actually virtual ref. sequences (computational ligation, contig stapling, etc.) is something we (i.e. Nathan Dunn) are just about to roll out soon in Apollo. It enables the curator to 'manually assemble' the contigs (correct order and orientation) to create a virtual ref. sequence.

I'll let either Moni or Nathan provide more details and an ETA for this imminent release

-S


On Fri, Apr 22, 2016 at 6:51 AM, Scott Cain <[hidden email]> wrote:
Hi Luca,

I'm cc'ing the JBrowse mailing list so people there can chime in too.

With JBrowse, you can visualize anything you want; all you need are coordinates of the features on the sequence you want to see (regardless of whether the sequence is "real" or not as you've suggested).  The only thing that you might want to do that JBrowse can't do is automatically map between different levels of assembly.  For example, if you have genes on contigs and the contigs mapped in to a scaffold, JBrowse can't automatically display the genes on the scaffold (but you can create a GFF file where you map the genes onto the scaffold).

There's no reason you can't show multiple levels of sequences in the same instance of JBrowse (contigs, scaffolds and LGs).  It would take some configuration to make clicking on contigs as they appear in a scaffold to take take you to that contig's JBrowse display, but it would not be terribly hard.  I suspect the hardest aspect of setting this JBrowse instance up will be getting the source data looking the way you want before you import it into JBrowse.

Please let us know if you have more questions.

Scott


On Fri, Apr 22, 2016 at 7:00 AM, Luca Bianco <[hidden email]> wrote:
Hello,

We are trying to use Jbrowse to visualize the information on the apple genome (Malus x Domestica) but we are hitting some problems. The genome is a high quality improved draft genome, which is heterozygous.

The current structure of the genome is organized as follows:
17 linkage groups  made by a number of scaffolds made by a number of contigs. We do not have the consensus sequence of scaffolds but only the approximate position (obtained through genetic markers) of contigs within scaffolds and that of scaffolds within LGs. 

Some scaffolds overlap some others and the same applies to contigs.

The problem we are facing is the fact that all the features refer to a refSeq (from you reference: "The reference sequences on which the browser will display annotations, and which provide a common coordinate system for all tracks"). 

If we understand the software correctly, the only sequence we are sure of is that of contigs but we would like to browse the genome LG by LG with the possibility of visualizing the scaffolding information down to the level of the contig for which we would like to access also sequence data. 

We are unsure on how to set this up on Jbrowse as if we specify the sequence of contigs then we have the correct information on the sequence but miss the higher level structures of scaffolds and LGs.
On the contrary, specifying LG level sequence would be highly imprecise and we would not be able to retrieve the correct contig sequence  in overlapping genomes.

Is it possible to specify a "fake" reference sequence (something like a string of Ns), but enabling the visualization of contig sequence when clicking on the contigs track?

Thanks for your help. Best Wishes,
Luca
  
--
Luca Bianco, Ph.D.
tel +39-0461615134
Computational Biology Department
FEM Research and Innovation Center
Via E. Mach,1
38010 San Michele all'Adige (TN)
Italy



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank" class="">216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
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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




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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
_______________________________________________
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