Chromosomes on physical and genetic maps

[Chevreau Julien]

Hello all,

I aim to input a physical and a genetic map (made with qtl) in qtl2 but I am unsure of the chromosomes fields meaning between the files :

For the physical map it's clear that the chromosome field represent the actual chromosomes.

For the genetic map, does the chromosome field refers to the linkage group number ? So the linkage group with more markers would end up with low numbers in the chromosome field, regardless of which chromosome they come from.

Thanks in advance for your help.

Warm regards,

Julien

[Karl Broman]

Markers need to have the same chromosome identifiers on the genetic maps that are used on the physical maps. The markers also need to be in the exact same order. The only difference between the two maps is that positions are in cM on the genetic map and in Mbp on the physical maps.

karl

[Chevreau Julien]

Thank you very much for your answer Karl !

Gonna report the chromosome identifiers for the linkage groups so.

Wouldn't have thought to sort both files by marker names.

Thanks again for your help and reactivity !

[Karl Broman]

The files shouldn't be sorted by marker names, but by their positions on the maps.

But the order of the markers on the physical map need to be the same as the order of markers on the genetic map: the two maps need to be consistent with each other, about the positions of markers. Only the inter-marker distances are different.

karl

[Chevreau Julien]

Right, ok.

As I aligned the reads and used this information to infer the linkage groups, marker order will not be changed.

Same maps, different units. Got it !

Thanks a lot Karl

Julien