isaacovercast
commented
1 year ago Hi David,
The clustering threshold actually is not used in the reference mapped assembly, so that explains why the results are the same. Let me know if you have other questions!
-isaac
Dear Isaac,
How exactly works the parameter Clustering Threshold in a reference mapped assembly? I am running Ipyrad under reference assembly method parameter, branching it for different threshold values (0.85 to 0.95, by 0,01 steps).
The point is that I am obtaining identical results (_stats.txt) and I am so confused about it, because It seems that modified CT parameter is not affecting in any way final results.
Best David