Problem With Consensus map

[Nikwan Shariatipour]

Hi

I'm new and I have 11 map file. Also I create one high density consensus map based on information from a paper not by Biomercator. I wounder should I create consensus map or not? If yes how I could merge the map files with the high density consensus map? Also can start QTL projection without creating consensus map? I tried to create a consensus map by biomercator with 6 files and high density map but I encountered  with 188 error?!! what is mean? Please give some advise..

Nikwan

[Yannick De-Oliveira]

Dear Nikwan,

 

Can you give me more information about your maps ? or maybe send me it to understand why you don’t success in compiling them.

 

However, you can indeed project QTLs without having a consensus map, the most important is to have common markers.

 

Best regards

Yannick

 

De : biome...@googlegroups.com [mailto:biome...@googlegroups.com] De la part de Nikwan Shariatipour
Envoyé : mardi 28 août 2018 01:50
À : biomercator <biome...@googlegroups.com>
Objet : [biomercator] Problem With Consensus map

 

Hi

 

I'm new and I have 11 map file. Also I create one high density consensus map based on information from a paper not by Biomercator. I wounder should I create consensus map or not? If yes how I could merge the map files with the high density consensus map? Also can start QTL projection without creating consensus map? I tried to create a consensus map by biomercator with 6 files and high density map but I encountered  with 188 error?!! what is mean? Please give some advise..

 

Nikwan

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[Nikwan shariati]

Dear Yannick

Hi

Sorry for delay answer. You can find my data in attachment. As you see I have some files and one reference map. I run biomercator 4.2 and in the first step I create the consensus map between files and reference map. Then I project the QTLs from all files except reference map on Consensus map. Then I go to run MetaQTL analysis step 1/2. In this step I choose my project, and then I choose consensus map as map, and chromosome and linkage group number 1B. Then I choose the regroup all traits (As you know my traits are Fe and Zn, which in chromosome 1 there are 4 QTLs for four traits in title GFe-1, GZnC-1, GZn-2 and GZn-3 but in meta-trait I put a different name (Like Micro)) and then I click on Next. 

In the second step I go to the metaQTL analysis step 2/2 and chosse the all parameter and then I determine the 5 the best and then Next. But when the analysis are going to run I will faced to an error which you can see in attachment. So please if possible to you tell me why the analysis not going run well and what is the problem. And also if possible please tell me about regroup traits and describe the way of using regrouping all traits and tell me about the details. 

My best regards

Nikwan

[z9655...@gmail.com]

Hi,Nikwan

I have met the same question.And I have tried many ways. Finally, I found out some reason. As I think that it is due to the number of QTL no enough, I have tried when I used 10 QTLs, the result would say" analysis failed",but when I used 11 QTLs,it became successful.That is so amazing,but i don't know if there are good way to solve the problem. I'm sorry my English is not well. I hope you can understand my means.

Zhengtong

在 2018年8月28日星期二 UTC+8上午7:50:02，Nikwan Shariatipour写道：