JoinSingles2All lists also alternative linkage groups with their LOD scores. So marker is put into LG 34 with LOD=23.8 but it could be in 3 or 4 (with much lower LOD, < 5). This information is not used by other modules but sometimes it is good to check. It can be useful for example when analysing very small datasets (say 8-20 individuals).
Cheers,
Pasi
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Thanks Pasi. I did not see that you had answered. So basically, JoinSingle2All said this :
If you asked for the high and technically allowing anything LOD of 30, SNP goes to Linkage Group 34.
If asked for a lower LO of 4.4 -> LG 3 and a lower again LOD of 3.3 -> LG 4
Many thanks,
I understand better the output now.
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Hello Pasi,
Not an issue this time as all is working fine.
I juste have a question on JoinSinglesAll Output.
What are the numbers after the linkage group ID for the marker integrated in a new linkage group as in this example :
34
0
34 23.811889455274443 3 4.410338025559511 4 3.3456959964294652
Are they LODscore ? Is the ordering indicative of what should be kept ?
Best regards,
Julien.
Dear Julien,
JoinSingles2All lists also alternative linkage groups with their LOD scores. So marker is put into LG 34 with LOD=23.8 but it could be in 3 or 4 (with much lower LOD, < 5). This information is not used by other modules but sometimes it is good to check. It can be useful for example when analysing very small datasets (say 8-20 individuals).
Cheers,
Pasi
Thanks Pasi. I did not see that you had answered. So basically, JoinSingle2All said this :
If you asked for the high and technically allowing anything LOD of 30, SNP goes to Linkage Group 34.
If asked for a lower LO of 4.4 -> LG 3 and a lower again LOD of 3.3 -> LG 4
Many thanks,
I understand better the output now.