Which tool is most reliable for QTL analysis of RIL population in Rice: QTL cartographer or ICIM?

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Jie-Yun Zhuang

Not matter which software you used, basically the same result should be produced. If the two tools generated different results based on your data, the only way to do is to check your data.

Vishnu Prasanth Vinukonda

Thank you for the answer. Kindly let me know, does ICIM is reliable software for mapping analysis in RILs?

Well, QTL cartographer has been used for many years and is widely accepted. You may first use QTL cartographer and evaluate if other tools are appropriate for your work.

Mohammad Anwar Khan

Apply software as per your requirements. if your objective is some highly variable trait QTL cartographer can a better choice for getting the extent of variation explained by each locus. If you are still getting complexity in your results you may try ICIM or others.

Saikumar Surapaneni

I think both are reliable software's for mapping QTLs. As i used both the software's for mapping , got similar results. Check your data once like input data files

Thank you Dr. JieYun Zhuang and Mr. saikumar.......Some problem in my input file. Found and corrected. Now getting similar results

Samantha Smarba

R/qtl is a good software and works well for RIL populations

Prahalada GD

Hi Katrina,

It is recommended that if your data is skewed you have to do data transformation depending upon the type of data you have (percentage data etc). You may use angular transformation methods for the transformation. Once after you finish data transformation you may use the data for the QTL analysis.