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CalabreseLab / seekr

A library for counting small kmer frequencies in nucleotide sequences.
http://seekr.org
MIT License
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Are the seekr available for the noncoding RNAs that are short than 200nt? #9

Closed Ci-TJ closed 5 years ago

Ci-TJ commented 5 years ago

Hello, I puzzled that seekr are available for the ncRNAs that are short than 200nt? And, in the literature you published, seekr were only applied for classing the function of lncRNAs. Best, Ci

Jessime commented 5 years ago

You can use seekr for shorter ncRNAs if you want. It isn't something that we've tried before, because there are other tools that may be better suited for predicting attributes of shorter RNAs. For example, it's easier to predict structure of short RNAs.

If you decide to use seekr for shorter RNAs, consider setting the kmer size to something small (maybe k=2 or 3), so that your matrix isn't too sparse.

Ci-TJ commented 5 years ago

Thanks! I will try this. Ci

Jessime commented 5 years ago

Good luck! I'll close this issue, but feel free to open another if anything doesn't work for you.