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jordenrabasco / Long_read_processing_tutorial

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[Section] Ecoli ASV identification #15

Open jordenrabasco opened 2 years ago

jordenrabasco commented 2 years ago

Here I show how to identify which ASVs belong to specific taxa. In this case Ecoli was identified since that is what you used in your previous tutorial.

https://github.com/jordenrabasco/Long_read_processing_tutorial/blob/afa1a962b305b79b0473a644cd9133a992bfa9ea/long%20read%20Tutorial.Rmd#L218-L228

benjjneb commented 2 years ago

There are several ASVs that are identified as E.coli but since we expect 3-6 unique alleles per strain, there are probably only 3-4 strains present.

This needs to be reworked with an eye to how we can usefully convey the idea of multiple strains and multiple alleles per strain.

jordenrabasco commented 2 years ago

forgot to link in commit statement b3f0ed0656181d6071c0ff8c6b3c1481b97d1386

Additionally I am a bit confused about how we differentiate stains in Ecoli specifically. There are conflicting statements online about the methodology. I included language about how i thought we did it (differentiate strains based on allele presence/absence) but I am less sure now.

jordenrabasco commented 2 years ago

The commit linked above is incorrect the correct one is here: 4de84cc4b21dc07a658c57501b2fd66e10220e73

Sorry for the confusion!

jordenrabasco commented 2 years ago

updated