In the beginning of the quality control tutorial we learn first how to exclude sequences by alignment. The output of the
qiime quality-control exclude-seqs process generates a suite of outputs, but I’m thinking that the
qc-mock-3-observed.qza files are not part of the output (rather, they are just part of the series of files downloaded in the beginning). Is this correct?
I’d like to be able to run the
qiime quality-control evaluate-composition function, but I’m not clear what this sentence is indicating:
Typically, feature composition will consist of taxonomy classifications or other semicolon-delimited feature annotations
The help menu indicates that it wants these to be
FeatureTable[RelativeFrequency] types, which, in the case of the observed data I certainly have. However, my mock communities aren’t from a manufacturer where the expected proportions are necessarily exact, thus I don’t know what to input/create for the expected data. Further, the mock community here is made of arthropod amplicons, and there absolutely is going to be some primer bias (so even if I knew something about the molarity of each mock member, it’s not particularly worthwhile except to demonstrate that there is primer bias, which, I guess is kind of neat neat…).
One thing I do have: multiple independent sequencing runs of the same mock community. I could generate a frequency table of expected numbers of reads using the average of each of these, but I’d probably want to normalize the counts first before doing something crazy like that.
Thanks for any advice on if and how to possibly implement.