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Published 20 hours ago • verified publisher icon GoekeLab

xpore/xpore/diffmod/model_kmer.csv

Open pa6774ac-s opened this issue 3 years ago • 2 comments

Hi! Cool tool! thanks! I was wondering how xpore/xpore/diffmod/model_kmer.csv was calculated. Thanks a lot!

pa6774ac-s avatar Sep 22 '20 23:09 pa6774ac-s

Hi @pa6774ac-s,

You're welcome!

The 'model_kmer.csv' file was obtained from Nanopolish output. It contains model_mean and model_std of all 1024 kmers from the Nanopolish model. So, we use them as a reference for signal distributions of unmodified kmers. However, you can create your own reference and give it to xpore. In this case, I will build an API in the future version for ease of use then. Thanks for raising this issue.

ploy-np avatar Sep 23 '20 02:09 ploy-np

Hi @ploy-np ,

I am also interested in the model_kmer.csv, as you mentioned which was got from nanopolish output. Do you mean run nanopolish eventalign and then statistics the results? May I ask what is the input?

Thanks in advance.  

loganylchen avatar Aug 23 '21 06:08 loganylchen