My SNP data has just arrived and I want to do my analysis for linkage mapping. I wonder that, how can I get arrange and prepare my data before analysis. Is there any instruction such as a tutorial or video explanation that I can benefit from it?
Hi Ugur,
it depends on the software you use (e.g. Joinmap) and the crossing type of your mapping polpulation (e.g. F2, BC1).
Which software will you use ?
Hi Stephan,
You are right. It's RIL popluplatıon and we are arguing to use JOİNMAP (slight possibility to use IciMAP, a free software)
Thanks
Hi Ugur,
It depends on what you mean! Do you mean creating genetic linkage maps? Then you can use Joinmap. However, if you mean linkage (QTL) mapping, then Joinmap is not the right software. I believe if you have license for Joinmap, you also have license for mapqtl. The later can be used for linkage (QTL) mapping. IciMap can do both, creating linkage maps and QTL mapping.
The R package 'onemap' is very good! And the vignettes are avaiable in the GitHub.
Hi Mohamed,
Yes you're right we have licence for both of them. And actually, the softwares are dont important, I just mean preparation of raw data for get ready to analysis. And I have got some research and I figure it out. Thanks for interest.
Best regards
Hi João,
R is so complicate for me now :). I have to consider it in more free time for later. Thanks for consideration.
Best regards
Hello Ugur,
Regarding onemap and R. This is the best time for you to learn R, and it will be an awesome skill for when you're done with your PhD, as well as a very good tool if you're doing genomics work.
I recommend trying it out for this project. The best time to learn a programming language is when you have a project to use what you learn on!
Hi Lorenzo
I will get consider your advice and thank you very much. Take care of yourself these days.
All the best
Uğur
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