Maximum and minimum read counts may not correspond to the original ASV/OTU/KO table because the original data file goes through some pre-processing steps during the data Sanity Check.
First, features whose total count across all samples is 1 are removed (since this is likely to be sequencing error or artifacts). Additionally, features that have a variance of 0 are dropped. Then the min/max number of OTUs >=2 are calculated from this filtered table. Note, the minimum sample count is the highest non-zero value.
Hello! I am not getting the “OTUs with ≥ 2 counts” in the data inspection. Does it mean that by default all OTUs with less than or equal 2 counts are filtered out from the downstream analysis? and next in data filtering, user can additionally filter by count to add more stringent filtration?
Data Inspection is just a summary of your data, nothing more.
Data Filtering allows you to control the actual filtering.
How Come that it tells you the number of otus(initial) and the number of outs with more than or equal 2 counts (which is a reduced number than the initial one), and that otu number is the one that will undergo further analysis including the filtration?
I feel a bit confused
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