Open rowi2024 opened 4 hours ago
Yes, this seems reasonable.
If you're running in consensus mode, you should be able to do this with the current breseq version. Add this option in addition to -x
to relax the default Nanopore filtering:
--consensus-reject-indel-homopolymer-length 0
However, it looks like you can't currently disable this in polymorphism mode b/c --polymorphism-no-indels
gets set.
We can update that in the next version.
Note to self: Also, it looks like the help text for the -x
option is a little broken. We could add some advice about making sure the base calling is done in high quality mode or adding back these options.
Thank you so much! That's great! I will add this and re-run it as soon as my current run of breseq is done:)
Good luck! Let me know if it doesn't work... these sets of options are not well-tested yet.
Hello, It is really great that Breseq can now work on Nanopore data! However, since basecalling has improved with recent upgrades to nanopore chemistries and basecalling models, I wonder if you might consider reducing the filtering of the homopolymer regions (allowing larger homopolymers to be queried for mutations). Thanks!!