Help

[Nikwan shariati]

Dear All

I prepared some Map and Qtl file which come from different analysis. Actually, I want to perform MetaQTL analysis in oerder to find meta QTL responsible for Fe and Zn quantity in wheat grains. So, i will go through the Biomercator tutorial but at the step   Meta QTL analysis  step 2/2 I will faced to this error message "End of analysis

Analysis failed
null".

If possible please run the MetaQTL analysis with my data and then tell me what is the problem?. I will be appreciate if somebody help me. 

Your Sincerely

Nikwan

[Nikwan shariati]

[Yannick De-Oliveira]

Dear nikwan

 

Can you tell me more about the previous steps ? Currently I didn’t succeded to build a consensus map or to project QTLs on the reference map (Somers_2004 I guess ?).

Anyway if you work on wheat did you tried to work with chr 1A 1B 1C etc considering them as real chromosome and not linkage groups of chromosome 1 ?

About the meta-analysis did you considered the kmax parameter ?  

 

Best regard,

 

--

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 Nikwan shariati
Envoyé : lundi 8 juillet 2019 18:47
À : biome...@googlegroups.com
Objet : [biomercator] Help

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[Nikwan shariati]

Dear Yannick

Many thanks for your reply. I go trough Biomercator V 4.2 tutorial and I built consensus map and also I succeeded to project QTLs but considering 

your answer I presume that I did analysis wrong. 

Dear Yannick I didn't understand Kmax parameter? What you mean about working with chromosome? You mean I remove lg from maps?

My best regards

Nikwan

To view this discussion on the web visit https://groups.google.com/d/msgid/biomercator/1bee1ff84a294865befee295f31e531e%40idfdcpripexmu02.inra.local.

[Yannick De-Oliveira]

Dear Nikwan,

 

The kmax is the maximum number of QTL clusters that metaQTL test for meta-analysis. You can set the kmax in the step 2 of meta-analysis.

The kmax value must be < to the total number of QTLs you have, by default kmax=10. Between, in your meta-analysis, even if you group all the traits under a meta-trait you  don’t have 10 QTLs, so you have to change this parameter when you launch the meta-analysis

About the chromosome I was just meaning to use

chr=1A

lg=1A

…

chr=1B

lg=1B

etc.

instead of

chr=1

lg=1A

…

chr=1

lg=1B

etc

But that shouldn’t change anything to the analysis just the organization in workspace

 

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 Nikwan shariati
Envoyé : mercredi 10 juillet 2019 15:51
À : biome...@googlegroups.com
Objet : Re: [biomercator] Help

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[Nikwan shariati]

OK my dear Yannick 

I will try to run the analysis again along with different kmax and also changing the lg. I will record the screen for display my analysis steps. 

If I failed again I will inform you. 

Your Sincerely

Nikwan

To view this discussion on the web visit https://groups.google.com/d/msgid/biomercator/37fa6e6f182e48189f3e4099cabe3ac6%40idfdcpripexmu02.inra.local.