Has anyone looked at the isolates whose phenotype and genotype don't match?

hollygene / CornellPostdoc

Various scripts I used during my tenure as a Postdoctoral Associate at Cornell University

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Has anyone looked at the isolates whose phenotype and genotype don't match? #8

Open hollygene opened 3 years ago

hollygene commented 3 years ago

genotype: resistant, phenotype, susceptible:
- is there another mutation that is counteracting the first? gene expr differences?
genotype: susceptible, phenotype: resistant:
- is there a new mutation that is conferring resistance?

hollygene commented 3 years ago

Using a k-mer approach could be useful for this - they are able to detect all kinds of variation Tools: SEER Bugwas PhenotypeSeeker Kover (reference-free) PySEER (SEER in python) HAWK DBGWAS - bridges gap between k-mers and SNPs