The output subgenomes are not paired

[ZhaoHang-bio]

Hi~,
I used this software to analyze the subgenome, input pairs of chromosome files, but output 11 chromosomes each and 13 chromosomes each. Is this result correct? What am I to make of this result?

look for you reply!
Hang

[zhangrengang]

Hi. It is true for some species, such as Brassica napus (9 and 10 chromosomes). Please show me your plots (at least the heatmap and circos plots) to have a check.

[ZhaoHang-bio]

Dear zhangrengang,

Thank you for your reply!

My heatmap and circos plot is below:

LG 21 and 23 are supposed to be a pair. But now it's in a subgenome.

here is the pca plot:

Hang

[zhangrengang]

LG21 seems to be incorrectly assigned, meaning that each subgenome should have 12 chromsomes. I suggest you reduce the -q to 50 or 100 to obtain more differentail kmers.

[ZhaoHang-bio]

It's seemly worked. Thank you for your help!