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