search

skovaka / UNCALLED

Raw nanopore signal mapper that enables real-time targeted sequencing
MIT License
520 stars 44 forks source link

CLARIFICATION: What is limiting UNCALLED from being evaluated for r9.4.1? #29

Closed harisankarsadasivan closed 3 years ago

harisankarsadasivan commented 3 years ago

wouldn't UNCALLED work if the kmer model is replaced with r9.4 (r9.4.1 seems to be unavaialble) and input dataset is from r9.4.1?

skovaka commented 3 years ago

UNCALLED works with r9.4.1. The signal characteristics are equivalent to r9.4, and UNCALLED has actually mainly been tested using r9.4.1 data. I'll update the README to reflect that.

If you have an ONT community account, you can find a slightly more in-depth answer here: https://community.nanoporetech.com/posts/a-minor-revision-to-r9-4-a-2108

harisankarsadasivan commented 3 years ago

@skovaka, thanks this helps. One last thing, did you observe 5mer model performs better than 6mer model or were they equivalent for event detection?

skovaka commented 3 years ago

They are pretty much equivalent. If you look at the means for 6-mers that have a 5bp suffix/prefix match you'll see they're nearly identical, indicating the 6th base doesn't add much information.

harisankarsadasivan commented 3 years ago

Thank you @skovaka