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zhangrengang / SubPhaser

Phase, partition and visualize subgenomes of a neoallopolyploid or hybrid based on the subgenome-specific repetitive kmers.
https://doi.org/10.1111/nph.18173
GNU General Public License v3.0
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Unbalanced of chromosomes number and differential kmers number among subgenomes #23

Open xingjianfeng100 opened 1 year ago

xingjianfeng100 commented 1 year ago

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

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 commented 1 year ago

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.