BCsFt switched alleles

[Noa BL]

Hello, 

Until now we have been constructing F2 maps guided by the extremely helpful rqtl tutorial. 

We are now starting to use F3 populations for qtl analysis and my question is - 

Is there a way to fix switched alleles in an F3 population with  BCsFt rqtl? 

Should i fix the switched alleles before running convert2bcsft? 

Thank you for your help,

Noa

[Karl Broman]

I think it won't make much difference, whether you do before or after.

karl

[Noa Bar]

Thank you for the reply!

I have another switched alleles question... 

when searching for qtls (after construction of the maps, which we do separately), can the search be affected if i have switched alleles? 

for example in the calculation of LOD scores, etc.. because i am comparing adjacent markers.. 

My worry is that i fix the switched alleles for the maps but then don't re-address them when i search for QTLs. 

Many thanks in advance

‫בתאריך יום א׳, 8 במאי 2022 ב-19:59 מאת ‪Karl Broman‬‏ <‪kbr...@gmail.com‬‏>:‬

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[Karl Broman]

If there are markers with the founder alleles switched, it will cause apparent double-crossovers around them, and will mess up the QTL analysis, so you want to fix them before doing QTL analysis.

karl