Comments (2)
Hi @Ge0rges, thanks for the pertinent suggestion. I'm also aware of work on RNA modification profiling by Nanopore. Anvi'o is currently limited in its ability to track genomic features beyond gene calls, but we are planning to soon implement a general framework for storing the coordinates of any type of genomic feature, like introns and exons, promoters, or modified nucleotides. Once we implement this, we'll get back in contact with you regarding what to do with modifications -- all of your suggestions sound perfect, and I'm glad to hear that there's a gap in the field that anvi'o can fill.
from anvio.
Sounds great! RNA modifications are definitely becoming a priority for ONT, and I think will open up a lot of interesting analyses. Let me know if I can be of any help.
from anvio.
Related Issues (20)
- [BUG] `anvi-get-sequences-for-hmm-hits` alignment silently fails HOT 20
- Skip checking genome hashes not working HOT 1
- anvio-8:mamba installation doesnโt work in the anaconda environment HOT 1
- [BUG] anvi-merge error (can I put multiple contigs.db in the code?) HOT 1
- [BUG] tarfile.ReadError: not a gzip file HOT 3
- [BUG] Nucleotide and amino acid not aligned in the inspect page HOT 3
- [REPORT] Updating anvi'o SCG taxonomy databases with new genes
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- anvio thinks the python version is different than the one installed HOT 3
- [BUG] Failed building wheel for datrie HOT 6
- [BUG] anvi-dereplicate-genomes python? error HOT 1
- [BUG] Incorrect (inflated) stepwise copy number for modules with complex parenthetical clauses HOT 1
- external gene call file created from more than two contigs HOT 5
- [BUG] anvi-estimate-scg-taxonomy crashes when external-genomes file contains contigs-db with old scg names HOT 8
- [BUG] anvi-pan-genome DIAMOND expected output files are missing
- [BUG] Memory issues with `anvi-estimate-metabolism` on large metagenomes in `--metagenome-mode` HOT 4
- [DISCUSSION] Common misconceptions and mistakes for anvi'o beginners that we should clarify in a blog post HOT 5
- [BUG] 'NumGenomesEstimator' sometimes double-counts some genomes as both Bacteria and Archaea HOT 8
- [BUG] Eggnog mapper not running in workflow, works fine manually in same conda env HOT 1
- [BUG] Key Error when running anvi-metabolism HOT 7
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