question about k-mer frequency

will-rowe / hulk

Histosketching Using Little Kmers

MIT License

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question about k-mer frequency #18

Open XiaomingXu1995 opened 4 years ago

XiaomingXu1995 commented 4 years ago

dear will-rowe, HULK is concerned about the k-mer frequency as described in your paper. I find that a minimizer hash value cannot be added into the minimizerSketch when it is contained in the sketch(minimizer.go, line 195). So the hash values in the minimizerSketch are unique. We cannot add the same minimizer hash value into the minimizerSketch inside a window, but if two different windows have the same minimizer-kmer, shall we concern the k-mer frequency?

will-rowe commented 4 years ago

Hi @XiaomingXu1995 - you are right that only unique minimizers are added to a sketch for a read. It would be a good idea to take into account minimizer frequency, I should probably try that.

I'm afraid HULK has been neglected recently. I will do my best to get back to it and try some new ideas out, including your observation. Thank you for your interest in it.

jianshu93 commented 3 years ago

Any update on this?

Thanks,

Jianshu

will-rowe commented 3 years ago

Hi Jianshu,

I'm afraid that I'm pushed for time at the moment and am unlikely to get to this anytime soon.

Will