Estimating genetic maps

[Oluyinka Ilesanmi]

Dear Dr Broman,

I am working on  mapping QTLs in a f2 population. I have 3,262 final markers that span 10 chromosomes with no missing data for all individuals. I tried generating the genetic maps on rqtl but the length is too long (about 1,500cM for one of the linkage groups).  I have drawn the maps earlier using Joinmap and the largest chromosome with about 308mbp gave a map of 250cM but I got lengthier maps on rqtl. Please how can I go about estimating the maps in rqtl? 

How can I be sure of ordering of the markers on each linkage group? 

After estimating the recombination fraction using "est.rf" and "checkAlleles", i get the response "No apparent problems".

Also, please what can you say about the recombination fractions and lod score in the attached images?

[Karl Broman]

See the tutorial on genetic map construction at https://rqtl.org/tutorials/geneticmaps.pdf

You want to look to see if there are particular markers that are causing the problem, and remove them.

karl

[Oluyinka Ilesanmi]

Dear Dr Broman,

Thank you for your response. The issue is that I cannot seem to find the markers that are causing the problem. 

The markers appear to be in the appropriate linkage groups and are not linked to another linkage group. Even when i use the "checkAllelles" , it says no apparent problems.

kind regards,

Yinka