Matrix-Count yielding oligos by individual sample reads, not oligos by overall sample

Commands in mothur
#1

Hello!
After I ran a set of samples through the mothur pipeline, my matrix-count table showed oligotypes per the individual sequence reads within each sample, not oligotypes by individual samples. What is causing this? How can I coerce mothur into collapsing the reads down by sample? Also, just so Im aware- what commands generates the Matrix-Count table?

Best,
E

#2

Sorry I don’t understand your question. mothur does not currently generate oligotypes. count.seqs and make.shared both make tables describing the number of sequences per sample by unique sequences and OTUs, respectively.

Pat