Unbalanced of chromosomes number and differential kmers number among subgenomes

[xingjianfeng100]

Hi~,
I have got a whole new set of problems now:

there is abnormally few subgenome-specific kmers in one of subgenomes, and the numbers of assigned chromosomes among subgenomes are abnormally unbalanced. I have also tried -k ( 8,13,15,17,22,27,33,37,45,50), -q (10,200,600,1000), -f(1.5,2), but failed to deal with this problem. Have you any suggestions about that?

[zhangrengang]

This issue may be normal for some species, and can be observed in poplar in our original paper. It may be beacause one of the subgenomes has had very few TE burst in its independent evolving period. It usually have no effect on the subgenome assignments, but the enrichments by sliding window may be useless.
By the way, you may set the number of subgenomes to 2, according to the cluster pattern.