Sidle -- extract reads with noncanonical nucleotide

[jwdebelius (Justine Debelius)]

Hi @jlli2000,

I shared this so everyone can see it. I is not a canonical nucleotide, and as far as I know q2-feature-classifier may not be set up to handle it. (Although you won't be able to build a tree, that step in Sidle won't be able to handle the I.)

There's a conversation about this issue here:

Importing BOLD COI sequence data into QIIME 2 / RESCRIPt

Hi @devonorourke, Sorry for the delayed response. Thanks for sharing the details of your awesome sleuthing process! About the primers not always landing where they should… this is the key problem I highlighted here, when it comes to using alignment positions for extraction, see the first bullet. It might be best to make a very small alignment, in which you know the primers will align properly, then start your process of mapping all your other data to this alignment. I’ve done this before and …

you might also check the BOLD database that's described here that will give you more ideas.

Building a COI database from BOLD references

Citations: If you use the following COI resources or RESCRIPt for COI database preparation, please cite the following: Michael S Robeson II, Devon R O’Rourke, Benjamin D Kaehler, Michal Ziemski, Matthew R Dillon, Jeffrey T Foster, Nicholas A Bokulich. RESCRIPt: Reproducible sequence taxonomy reference database management for the masses. bioRxiv 2020.10.05.326504;…

I'm sorry I dont have any COI experience, so I'm not sure about this particular issue.

Best,
Justine