methylated Guanine (mG)

[eltonjrv]

Issue Report

Brief question/probing

Please describe the issue:

I wonder if there's any upcoming 7mG modification model to be applied for rRNAs' direct RNA-seq. I'm currently using differr (https://github.com/bartongroup/differr_nanopore_DRS) but results are not too compelling in some cases. Any other recommendations would be appreciated. Thanks, Elton

[a-slide]

Hi Elton, Unfortunatly, m7G is not commercially available as a phosphoramidite monomer, which is required for us to generate the training material. I am told by our chemists that it would be very challenging to synthesize. Hence we will very likely not include this one in our offering any soon. On the other end, we are currently working on all 4 2'Ome modified nucleotides, which might also be of interest for your work. Thank you

[eltonjrv]

Thanks for your reply, Adrien (and nice chatting again with you :) Good to know on the upcoming 2'O methylation model. We'll definitely use it for assessing ncRNAs through DRS. So, I believe as of now I should keep relying on differential error rate approaches for m7G cases. Thanks again and I'm sure we'll keep in touch, Warm regards, Elton

[a-slide]

Yes I can confirm that the current basecalling model should not have seen many instances of m7G and hence should be making errors in some cases, but you probably know that basecalling errors are not always a very reliable proxy for modified bases. If you would like to go a bit deeper you could also run a signal comparison analysis, if you have a control sample without m7G. There are community tools for this such as Xpore and Nanocompore, and you can also run a quick analysis with Remora API https://github.com/nanoporetech/remora/blob/master/notebooks/metrics_api.ipynb

[eltonjrv]

Thanks again, Adrien. Yes, we do have a knock-down for the m7G writer under assessment. I'll give Xpore and Nanocompore a try. Best, Elton