Biomercator v4 results query

[mukesh choudhary]

I have carried out MetaQTL analysis in Biomercator V4 successfully. But have few queries regarding attached file of results (Capture 1) and to prepare a Table published in one of the MetaQTL manuscript (Capture 2)

 

1. The individual QTLs falling in one metaQTL are showing few traces of colours (overlapping type) with adjacent metaQTLs . How to deal with this problem? (Capture 1)

2. In our case, the experiments used for metaQTL analysis contains the Lower and Upper Confidence Intervals (CI) and we have used this data for QTL filr preparation. Do we need to take the average of these CI for estimating the mean initial CI or have to take the average of CI for individual QTLs provided in Biomercator result file ? I want to prepare a table given in Capture 2  (Column 9) (in one of the published paper)

3.Do we take the average of PVE for individual QTLs falling under particular metaQTL for estimating the PVE for that particular metaQTL? Capture 2  (Column 8) (in published paper). 

4. For MetaQTL CI calculation do we need to take the mean of lower CI and Upper CI obtained in Biomercator v4 result file? Capture 2 (Column 10) 

5.The flanking markers are far away from end points of metaQTL regions means not exist as perfect flanking markers. The distance between the flanking markers does not exceed 10 cM. Can we use these far away flanking markers ? If not, what is the alternative option?

Looking for a quick response 

Thanks

[Yannick De-Oliveira]

Dear Mukesh Choudhary,

 

1-      This is not really a problem, it is the result of the clustering step. For some QTLs the clustering is not able to determine at 100% if the QTLs explain a metaQTL or another.

2-      I guess you can use the ones provided by BioMercator

3-      Concerning the PVE you can estimate it with the mean of former QTLs, but I’m not sure about QTLs that don’t explain a metaQTLs at 100% (ie your first question) maybe for this QTLs you can weight the former value of the PVE to estimate the mean for these QTLs

4-      You don’t have to calculate it, BioMercator provide these values in the ‘table.txt’ file of the meta-analysis

5-      I’m sorry for this question, I’m not sure to understand what you want to do with the flanking markers and the metaQTLs ?

 

Best

Yannick

 

PS : please do not hesitate to use the new forum for BioMercator :

https://sourcesup.renater.fr/forum/?group_id=2301

 

 

--

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 mukesh choudhary
Envoyé : mercredi 12 juin 2019 08:15
À : biomercator <biome...@googlegroups.com>
Objet : [biomercator] Biomercator v4 results query

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[mukesh choudhary]

Thanks for kind reply

Regarding step 5, I just wanted to know that suppose the MetaQTLs obtained in results have flanking markers a bit away (means not too close), then is it fair to report only those markers as flanking markers. We faced such issues for some MetaQTLs inspite of using the latest reference map. Please clarify this.

One more query is regarding the structural, functional annotations and anchor file for maize. What are basic steps or strategy to make the anchorage file? Please explain with sources to be used and it will be great favour, if you can explain with an example.

Thanks a lot

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[Yannick De-Oliveira]

Dear Mukesh Choudhary,

 

I guess using these flanking markers is correct, it is more a matter of confidence. The closer are the flanking marker the better it is, but using the closest ones is the the way you should do it. I hope to answer to your question.

 

Building the anchorage file is probably most difficult step because you will have to find in public database (if you don’t have the info) physical position of markers located in the genetic maps you are working with. This kind of database will depend mostly of the species you are studying. For example for maize we can use maizegdb to find such information (https://www.maizegdb.org/)

 

Best regard

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 mukesh choudhary
Envoyé : mardi 18 juin 2019 11:50
À : biome...@googlegroups.com
Objet : Re: [biomercator] Biomercator v4 results query

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