Question: Kmergenie fails to fit models with --diploid settings
gravatar for pepijn.kooij
4.5 years ago by
Royal Botanic Gardens, Kew
pepijn.kooij0 wrote:

I’ve been trying to run kmergenie on a trimmed dataset of MiSeq 2x300 paired end reads (trimmed with trimmomatic), using a list with the forward and reverse, paired and unpaired output from trimmomatic. When I run kmergenie with the normal haploid settings it works fine, but running it with --diploid many of the many of the kmer models are not able to fit the on the histograms (see screenshot of terminal+html files). Any idea why this is?

screenshot of terminal

results without --diploid

results with --diploid

I really would like to be able to fit the diploid models, which I think would improve the kmer estimations, based on the fact that you can clearly see two humps in the histograms.

Hope you can help me out with this.

miseq kmergenie paired-end kmer • 1.6k views
ADD COMMENTlink modified 3.6 years ago by Rayan Chikhi1.4k • written 4.5 years ago by pepijn.kooij0
gravatar for Rayan Chikhi
3.6 years ago by
Rayan Chikhi1.4k
France, Lille, CNRS
Rayan Chikhi1.4k wrote:

for the record: Pepijn and I communicated by email, and the diploid model has been improved in recent kmergenie versions, hopefully addressing this issue.

ADD COMMENTlink written 3.6 years ago by Rayan Chikhi1.4k
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