BioMercator v4.2 : New release now available

[Yannick De Oliveira]

Dear users,

We are glad to announce you that the new release of BioMercator is now available.
This new version allow user to upload physical map informations in BioMercator.
To do this :
1- You need the structural annotation file of the genome in GFF format
2- You can add functional annotations from the GO informations
3- You need an anchor file to align your physical map and your genetic map

All those files are described in the documentation and in the test dataset

regards,
Yannick

[Yahui Wu]

So nice to hear of that!

Thanks very much!

在 2013年7月24日星期三UTC+8下午10时42分45秒，Yannick De Oliveira写道：

[Yannick De Oliveira]

Here is a Valid link to download BioMercator V4.2 :

http://moulon.inra.fr/index.php/fr/seminairedoc/doc_download/64-biomercator-v4

[Stella Salvo]

Is anyone else having trouble loading annotations?  I'm downloading maize files from maizesequence.org, but V4.2 is not reading it correctly.

Best wishes,

Stella

[Yannick De Oliveira]

Dear Stella,

Could you check that the files you downloaded has the same format than the files described in the folder Tests Datasets/Physic Files/ ?

Best regards
Yannick

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Yannick de Oliveira
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91190 Gif-sur-Yvette
Tel : 01.69.33.23.78 

[Stella Salvo]

Hi Yannick,

Yes, they have the same format as in the physic folder.  I tried to load those as well, but the import wizard showed weird symbols in lieu of text.

Best wishes,

Stella

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Stella Salvo

Ph.D. Candidate

Monsanto Fellow

 

University of Wisconsin-Madison

Department of Agronomy

1575 Linden Drive

Madison, WI 53706

Lab: (608) 262-6521

Cell: (949) 698-2163

Fax: (608) 262-5217

Email: ssa...@wisc.edu

[Yannick De Oliveira]

Dear Stella

Can you send me the link or the files themself that you downloaded ?

Regards
Yannick

[Stella Salvo]

Hi Yannick,

They were too large to send as an attachment.  I used the two files that were available in the V4.2 download in the physics file.  I also tried the same files from maizesequence.org.  I downloaded ZmB73_5b_FGS.gff.gz and ZmB73_5a_xref.txt.gz directly from http://ftp.maizesequence.org/current/filtered-set/ and http://ftp.maizesequence.org/current/functional-annotations/, respectively.

If at all possible, were you able to get a consensus map on the files I send you yesterday?

Many thanks and best wishes,

Stella

On Tue, Oct 8, 2013 at 9:34 AM, Stella Salvo <stella...@gmail.com> wrote:

Hi Yannick,

Below are the files I used.  They were available in the V4.2 download, but also I retrieved them from the maizesequence.org ftp site that is listed in the tutorialv4_en.pdf

Best wishes,

Stella

[Yannick De Oliveira]

Dear Stella,

Did you used an anchor file ? With the files i downloaded on the maizesequence site (which is the same as Dataset provided with BioMercator) I succeeded to upload them in BioMercator. But, you absolutely need an anchor file to use this genome version.

Concerning your maps, I corrected a bug in the metaqtl package, i need to go further in my tests to be sure this correction didn't impact the rest of the code. Anyway when I compiled your maps, no map were compiled for your linkage group 1 while it is connected. So, I need to talk with genetician researcher of my lab to see what is happening ...
As soon as everything is back to normal, I will put a new version to download with the bug correction

Regards,
Yannick

[Stella Salvo]

Hi Yannick,

Yes, I used the anchor file available in the dataset provided by BioMercator.  Perhaps I'll try a different computer...

Many thanks for the follow-up.  I'm looking forward to your findings.

Best wishes,

Stella

[Yannick De Oliveira]

Hello Stella,

If you have again some problems can you make a screenshot of the message you have ?
Regards,
Yannick

[Stella Salvo]

Hi Yannick,

This is the screenshot when trying to import the FGS gz file.

Best wishes,

Stella

[Yannick De Oliveira]

Hi Stella,

Ok I think I understand what happened. I think you didn't unziped the file you downloaded

Regards
Yannick

[Stella Salvo]

Hi Yannick,

You are correct!  Sorry for that.  I unzipped and retrieved the functional annotation file: xref.txt (19,684 KB in size) and the structural annotation file ZmB73_5b_FGS.gff (85,642 KB).  I loaded these with the anchor and the genome view looks great on V4.2.

Many thanks and best wishes,

Stella

[Neeraja C N]

hello, dr.oliveira,

recently i have downloaded biomercator version 4 and wanted to identify MQTL for nitrogen use efficiency in rice. i could make the map files and qtl files following manuals.

but when i'm trying to construct consensus map, a small figure is appearing, instead of map. i've attached the screen shot for your information.

please help.

regards

neeraja

[Yannick De Oliveira]

Dear Neeraja,

Can you send me your files that i have a look to them ?

regards
Yannick

[Neeraja C N]

dear dr.yannick,

sorry for the late response. now i'm able to construct map and identify QTL clusters and go up to MetaQTL-QTLclustinfo 1/2

but when i tried to do MetaQTL-QTLclustinfo 2/2

i get the following message

Analysis starting

End of analysis

Analysis failed

null.

are there no metaQTL?

please help

neeraja

 

neeraja

-- <b

...

[Neeraja C N]

dear dr.yannick,

under QTL meta-analyses with Metanalysis (Gerber & Goffinet), i'm getting the results. only with MetaQTL-QTLclustinfo 2/2, it says null 

please help

wishes

neeraja 

[Neeraja C N]

dear dr.yannick,

the software biomercator is working now.

thank you

neeraja

[Fabrizio Costa]

Dear Yannink,

I a new BioMercator users and I am having trouble in the creation of a pre-consensus map, since all the linkage groups are not shown and the markers have all the position set to 0, even if the connectivity value for all my LGs are true.

How can I resolve this issue?

Many reagrds

fabrizio

[Yannick De Oliveira]

Dear Fabrizio,

Can you send me your maps that i can have a look to them ?

best regards
Yannick

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[Virginie]

Dear Fabrizio,

 

I have the same problem as you for the creation of the consensus map. All markers have the position set to 0, even if the connectivity values are true.

 

Did you find the solution ?

 

Best regards,

 

Virginie

Le mercredi 24 juillet 2013 16:42:45 UTC+2, Yannick De Oliveira a écrit :

[Anuj Kumar]

Dear Dr Yannick,

I am working on meta analysis using BiomercatorV4 and  I arranged data into two separate files(map and QTL) as given  in tutorial's example files. Whenever I upload them into Biomercator V4, I get two map files even I already checked so many times both files but I did not find any space or tab in map name. If I drag the second map, I see only small LG bars without markers. I am attaching both files. Plz have a look at both files if they have any mistake.

Thanks 

Anuj Kumar

University of Arkansas

Fayetteville, Arkansas, USA

[Anuj Kumar]

Dear Dr Yannick,

I am working on meta analysis using BiomercatorV4 and  I arranged data into two separate files(map and QTL) as given  in tutorial's example files. Whenever I upload them into Biomercator V4, I get two map files even I already checked so many times both files but I did not find any space or tab in map name. If I drag the second map, I see only small LG bars without markers. I am attaching both files. Plz have a look at both files if they have any mistake.

Thanks 

Anuj Kumar

University of Arkansas

Fayetteville, Arkansas, USA

[Yannick De Oliveira]

Dear Anuj Kumar,

In the field mapName of both files, it seems you have some tabulations after the name of the map, if you open your file with a simple text editor (not Excel or any Excel like) you should be able to delete them easily.
In the same way, every tabulation at the end of a line must be deleted in both files.

best regards
Yannick

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Yannick DE OLIVEIRA
IE Bioinformatique - INRA
Génétique Quantitative et Évolution – Le Moulon
INRA – Université Paris-Sud – CNRS – AgroParisTech
Ferme du Moulon
91190 Gif-sur-Yvette
France
http://moulon.inra.fr/

[Anuj Kumar]

Dear Dr Yannick,

Thank you very much for your quick reply. I appreciate it. If I have any problem regarding Biomercator V4, I will ask you again.

Thanks Again

Anuj Kumar

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ANUJ KUMAR
Monsanto's Beachell-Borlaug International Research Scholar
Crop, Soil & Environmental Science(CSES)
115 Plant Science Building,
University of Arkansas,Fayetteville,AR-72701,USA
Email id: anujbio...@gmail.com 

              axk...@uark.edu 
Phone# +1-479-684-1434(M)

            +1-479-575-5734(Lab)

Website :http://plantstress-pereira.uark.edu:8080/PlantSciences/#team  

“Hunger is not an issue of charity even it is an issue of justice so as a Plant Molecular Breeder, fights against the hunger and feeds the world”

[Anuj Kumar]

Dear Dr Yannick

Thank you for suggestion to remove the tabs using text editor. I did it and it worked fine. However, when I load my original files(map file and qtl file), the software works fine until second step but it doesn't go to third step for finishing the loading the files into software. I think my qtl file is very huge because it has almost 1300 qtls. Can it be a problem for this software? Please have a look at my both files and please give your useful suggestions. I look forward for a quick response.

Thanks 

Anuj Kumar

[Yannick De Oliveira]

Dear Anuj Kumar,

Can you try to launch BioMercator in a terminal with this command line (you can find it in the User guide) :

java -jar -Xmx1024m BioMercatorVxx.jar

The -Xmx argument can increase memory usage. If you have a memory leak you should see it also in the terminal

Best regards
Yannick

[Anuj Kumar]

Thank you Dr Yannick. I did it and it is running pretty smooth.

Thanks

Anuj Kumar 

[Satish Yadava]

Dear Dr. Yannick,

I have earlier used version 2 of BioMercator and now trying to analyse another  data with version 4.

I have a query related to map file:

In the 'locusLocation' there are two possibilities - relative and absolute.

What do these mean ?

Do they mean the positions in terms of interval between consecutive markers for for 'Relative' ?

And how do I decide the quality of my map ? Should it be simply based on number of markers in a map ?

Thank you.

[刘伟]

That is really good tools. However, I want to know if you can also provide some files needed for these analysis. Such as GFF and GO information for modle organism rice. Thanks.

[Yannick De-Oliveira]

Dear user,

 

Thank you for your comments on BioMercator. I already thought about that but realized it is difficult to provide files for structural and functional annotation. First, the structural annotation (GFF) must be consistent with the genetic maps you load in BioMercator (I mean the chromosome names must be the same). Secondly , the functional annotation can be different from a project/consortium to another and it is difficult to choose one.

 

Best regards,

 

Yannick DE OLIVEIRA

IE Bioinformatique - INRA

Génétique Quantitative et Évolution – Le Moulon

INRA – Université Paris-Sud – CNRS – AgroParisTech

Ferme du Moulon

91190 Gif-sur-Yvette

France

+331.69.33.23.76

 

De : biome...@googlegroups.com [mailto:biome...@googlegroups.com] De la part de ??
Envoyé : dimanche 15 janvier 2017 14:01
À : biomercator <biome...@googlegroups.com>
Objet : [biomercator] Re: BioMercator v4.2 : New release now available

--

[刘伟]

Hi sir,

      Happy new year. I have a question that confuse me. I used the Cornell rice genetic map as the reference map, and want to merge other published genetic map. So I use the Consmap function and merge all these maps from paper with Cornell map as reference, however, some SSR markers have a negative genetic distance at the begining of chromosome in the consmap. The instruction of Biomercator does not provide much details about the issue. Can you kindly provide some advices about the problem?

Sincerely,

Wei

2017-01-24 23:44 GMT+08:00 Yannick De-Oliveira <yannick.d...@inra.fr>:

Dear user,

 

Thank you for your comments on BioMercator. I already thought about that but realized it is difficult to provide files for structural and functional annotation. First, the structural annotation (GFF) must be consistent with the genetic maps you load in BioMercator (I mean the chromosome names must be the same). Secondly , the functional annotation can be different from a project/consortium to another and it is difficult to choose one.

 

Best regards,

 

Yannick DE OLIVEIRA

IE Bioinformatique - INRA

Génétique Quantitative et Évolution – Le Moulon

INRA – Université Paris-Sud – CNRS – AgroParisTech

Ferme du Moulon

91190 Gif-sur-Yvette

France

+331.69.33.23.76

 

De : biome...@googlegroups.com [mailto:biomercator@googlegroups.com] De la part de ??

Envoyé : dimanche 15 janvier 2017 14:01
À : biomercator <biome...@googlegroups.com>
Objet : [biomercator] Re: BioMercator v4.2 : New release now available

 

That is really good tools. However, I want to know if you can also provide some files needed for these analysis. Such as GFF and GO information for modle organism rice. Thanks.

On Wednesday, July 24, 2013 at 10:42:45 PM UTC+8, Yannick De Oliveira wrote:

Dear users,

We are glad to announce you that the new release of BioMercator is now available.
This new version allow user to upload physical map informations in BioMercator.
To do this :
1- You need the structural annotation file of the genome in GFF format
2- You can add functional annotations from the GO informations
3- You need an anchor file to align your physical map and your genetic map

All those files are described in the documentation and in the test dataset

regards,
Yannick

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[Yannick De-Oliveira]

Dear Wei,

 

The problem you describe can happen in some situation, for example  :

 

On one of your map you have a marker A at a position of 0 cm and a marker B let’s say at a position of 3cm

On your reference map your marker B is positioned at 0cm, when you compile your maps with the reference map the new position of the marker A in the consensus map can be negative.

 

Best regards,

Yannick

 

Yannick DE OLIVEIRA

IE Bioinformatique - INRA

Génétique Quantitative et Évolution – Le Moulon

INRA – Université Paris-Sud – CNRS – AgroParisTech

Ferme du Moulon

91190 Gif-sur-Yvette

France

+331.69.33.23.76

 

De : biome...@googlegroups.com [mailto:biome...@googlegroups.com] De la part de ??
Envoyé : samedi 28 janvier 2017 16:20
À : biome...@googlegroups.com
Objet : Re: [biomercator] Re: BioMercator v4.2 : New release now available

 

Hi sir,

 

      Happy new year. I have a question that confuse me. I used the Cornell rice genetic map as the reference map, and want to merge other published genetic map. So I use the Consmap function and merge all these maps from paper with Cornell map as reference, however, some SSR markers have a negative genetic distance at the begining of chromosome in the consmap. The instruction of Biomercator does not provide much details about the issue. Can you kindly provide some advices about the problem?

 

Sincerely,

Wei

2017-01-24 23:44 GMT+08:00 Yannick De-Oliveira <yannick.d...@inra.fr>:

Dear user,

 

Thank you for your comments on BioMercator. I already thought about that but realized it is difficult to provide files for structural and functional annotation. First, the structural annotation (GFF) must be consistent with the genetic maps you load in BioMercator (I mean the chromosome names must be the same). Secondly , the functional annotation can be different from a project/consortium to another and it is difficult to choose one.

 

Best regards,

 

Yannick DE OLIVEIRA

IE Bioinformatique - INRA

Génétique Quantitative et Évolution – Le Moulon

INRA – Université Paris-Sud – CNRS – AgroParisTech

Ferme du Moulon

91190 Gif-sur-Yvette

France

+331.69.33.23.76

 

De : biome...@googlegroups.com [mailto:biome...@googlegroups.com] De la part de ??

Envoyé : dimanche 15 janvier 2017 14:01
À : biomercator <biome...@googlegroups.com>
Objet : [biomercator] Re: BioMercator v4.2 : New release now available

 

That is really good tools. However, I want to know if you can also provide some files needed for these analysis. Such as GFF and GO information for modle organism rice. Thanks.

On Wednesday, July 24, 2013 at 10:42:45 PM UTC+8, Yannick De Oliveira wrote:

Dear users,

We are glad to announce you that the new release of BioMercator is now available.
This new version allow user to upload physical map informations in BioMercator.
To do this :
1- You need the structural annotation file of the genome in GFF format
2- You can add functional annotations from the GO informations
3- You need an anchor file to align your physical map and your genetic map

All those files are described in the documentation and in the test dataset

regards,
Yannick

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