search

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
53 stars 12 forks source link

No differential kmers #26

Open xychen233 opened 9 months ago

xychen233 commented 9 months ago

Hi,

I am trying to use the SubPhaser to phase the subgenomes of my species. However, after filtering differential kmers, no differential kmers were remained. I used parameter of this -k 15 -q 50 -f 2 . The same result is achieved even if I continue to reduce -k and -q.

23-12-27 17:32:21 [INFO] 125035 kmers in total 23-12-27 17:32:21 [INFO] Filtering differential kmers 23-12-27 17:32:22 [INFO] Start Pool with 112 process(es) 23-12-27 17:32:25 [INFO] After filtering, remained 0 (0.00%) differential (freq >= 25) and 0 (0.00%) candidate (freq > 0) kmers

Do you have any suggestions?

thanks, Chen

zhangrengang commented 9 months ago

Does your genome behave like an autopolyploid? Or refer to https://github.com/zhangrengang/subphaser#When-SubPhaser-do-not-work for other possible reasons.

xychen233 commented 9 months ago

Thank you for your answer!