How to project QTLs collected from different papers onto an existing integrated map?

[kyc92...@gmail.com]

Hi,

I just come across a problem as mentioned by title, now i have an integrated genetic map (it is sort of consensus map including different marker types generated from different genetic maps) and QTLs info (their flaking markers can be found in that integrated map). But the problems are that:

• integrated map does not have crosstype, pop size as well as linkage group info
  
• QTLs are collected from different pop from previously published papers, so info of those is really inconsistent. Now i only have their Chr, flanking makers, variance explained by this QTL (not all are given, some are not available)

I want to present these QTLs in integrated map, so how to manage their input formats so could be visualised and project properly? Any other info of QTLs and integrated map required for this purpose?

regards,

Yichen

[Praveen Khatri]

I think there is no problem if you are project qtls collected from different sources on to a single map generated with all the markers from a source

[kyc92...@gmail.com]

Actually i failed to input the map file, could be any of problems below:

• improper marker location (the location of first three or four markers is minus something)
• No LG
• unknown info in terms of some mandatory properties

Attached one is a part of my map file, could you please help me look at it?

regards,

Yichen

在 2018年10月24日星期三 UTC+11下午2:01:36，Praveen Khatri写道：

[Shilpi Dixit (CO-IN)]

There is unseen spaces in the input file, remove using notepad++

I think this will work

 

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[kyc92...@gmail.com]

Hi again, i found it worked after LG given (though LG is the same as chr in my case). Just wonder if this sort of manually setting LG is ok and will not affect QTL projection later on?

[Praveen Khatri]

Hi

have you got the marker location from any website or calculated by yourself. This is not the right way to arrange markers

I my sense.

1. arrange all markers in excel and sort them from lower to higher value separately for each chromosome/Lg

2. calculate interval between successive markers and then add them to biomercator

Regards

Praveen

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[kyc92...@gmail.com]

hi this genetic map actually is merged from different consensus maps and already published by researchers, all marker locations are arranged in order, not done by myself. I am just confused by the LG, because no way to calculate LG in this map, and there might be many LGs in same Chr, so i am unsure if it is ok to indicate LG just the way for Chr. Now i have visualised the QTLs on that integrated map, and it seems nothing wrong. So it probably works and LG does not matter in my case (just deem as chr).

Cheers,

Yichen 
在 2018年10月24日星期三 UTC+11下午3:46:26，Praveen Khatri写道：

[Praveen Khatri]

I think this might work.. If u r getting all qtl projected on same map... 

For mera analysis our primary goal was to determine the location of flanking markers nothing else. If you are getting marker information flanking your qtl than its totally fine

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[kyc92...@gmail.com]

Thanks Praveen, sorry for my heaps of questions. In terms of some QTLs without LOD value, they could lead to input failure of the whole QTL file (remove these QTLs, file can be processed with no worries). Is this because LOD value is a MUST input attribute? I tried 'null' under the LOD column for QTL with no LOD, it did not work, any way to get it fixed?

在 2018年10月24日星期三 UTC+11下午7:14:34，Praveen Khatri写道：

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[Yannick De-Oliveira]

Dear Ychen,

If I understand well your problem you have only flanking marker of your QTls ? No genetic position on any map that's it ?

-----Message d'origine-----
De : biome...@googlegroups.com [mailto:biome...@googlegroups.com] De la part de Praveen Khatri
Envoyé : mercredi 24 octobre 2018 05:02
À : biomercator <biome...@googlegroups.com>
Objet : [biomercator] How to project QTLs collected from different papers onto an existing integrated map?

I think there is no problem if you are project qtls collected from different sources on to a single map generated with all the markers from a source

[Yannick De-Oliveira]

Dear Ychen,

 

When you have a whole chromosome, just give the same name to your LG (ie LG = chromosome). This will have no effect on QTLs projection

 

Best regards

Yannick

 

De : biome...@googlegroups.com [mailto:biome...@googlegroups.com] De la part de kyc92...@gmail.com
Envoyé : mercredi 24 octobre 2018 07:09
À : biomercator <biome...@googlegroups.com>
Objet : Re: [biomercator] Re: How to project QTLs collected from different papers onto an existing integrated map?

[kyc92...@gmail.com]

Thanks Yannick, u r right and this is how i could successfully input and visualise map data, now i have no problem with genetic map. The only annoying thing is the QTL file since some QTLs with no LOD value available from previous publications, but apparently LOD is mandatory and can not be blank in QTL file, so i wrote down "null" instead but still can not read QTL file. Because i want to project all these QTLs onto map, so just checking how could i get this done otherwise i will have to leave them.

best regards,

Yichen  

在 2018年10月29日星期一 UTC+11下午9:08:27，Yannick De Oliveira写道：

[kyc92...@gmail.com]

Hi again, I have both flanking marker of QTLs as well as their corresponding location on genetic map, but i do not have LOD score for a handful of QTLs. So this caused QTL file input failure. If i remove these QTLs, the software can read QTL file with no problem. So i want to know how could we deal with missing data rather than deleting them.

在 2018年10月29日星期一 UTC+11下午9:05:48，Yannick De Oliveira写道：