use for RtN for long reads

[eesiribloom]

I am interested in the concept of extracting mitochondrial reads from nanopore long-read data. Would RtN be suitable for this?

[Ahhgust]

Who knows! I've never worked with nanopore data before, but if my limited knowledge is (more or less) right, I'd wager that there are probably better ways to go about identifying and/or removing Numts that better leverage the technology.
For example, if you're getting reads that are >16kb, you should be getting signal that is amenable to circular alignment (real mito data) or has good local alignment to the autosomes (Numt-- eg, you sequenced through the mito sequence inserted in the autosomes and into something that is clearly autosomal instead). Read mappers that do local alignment (near all, these days) should give you that information (but I would pay attention to the Numts that are already annotated as such in the reference genome; eg, I'd ignore local alignments to the autosomes that intersect the regions outlined here: https://github.com/Koumokuyou/NUMTs)
Make sense?
And sorry about the delay in correspondence; Thanksgiving + the end of the semester has left me a bit behind schedule.
Please let me know if you have other questions, are need help getting this ball rolling.
-August

[eesiribloom]

Hi August, thanks for the response. That makes sense. so if you have reads that are likely spanning NUMTs and adjacent autosomal sequences, you may not actually need to remove NUMT sequences in the same manner?

[Ahhgust]

That's the short of it. To add, what I just described is an idea. Whether or not it works is a separate issue. Removing reads that have (non-trivial) alignments to the autosomes is something you can do with a bit of grep and samtools, however. If you want/need help, or a rough sketch of how to do that, just let me know.
-August