Closed gavinmdouglas closed 11 months ago
Thanks for reaching out!
I have not explored that deeply, no, so can't comment about robustness directly, but I do have some intuition and related thoughts worth mentioning.
I hope these thoughts are useful (and I hope StrainFacts is useful, too)!
Thanks Byron, that's very helpful! I'm going to see how things change with and without prevalence cut-offs for the data I'm using... I'll keep your advice in mind.
Cheers,
Gavin
Hey Byron,
I hope all is well with you! Just a quick question -- in your
filter_data.ipynb
notebook you pre-processed the example data so that polymorphic sites found in < 5% of samples were excluded. Have you explored how robust StrainFacts is when this filtering step isn't performed? I'm actually interested in strains that might be sample-specific (and as long as they are at sufficient depth in that sample I'm not too worried about false positives).Thanks!
Gavin