Output table of OTUs with taxonomic ID by sample?

Hi all,

I’ve just finished clustering and classifying OTUs for my 16S amplicon data following the MiSeq SOP for the first time. I’d like to output a table showing OTU abundance (with taxonomic identification) for all of my libraries. Is there an easy way to do this? I have a count_table file that contains a distribution of representative read names across all my samples, but no OTUs or taxonomy. My cons.taxonomy file shows OTUs and taxonomy, but only with total abundance across all samples. Is there a way to smush them together?


If you still have the list file generated during OTU clustering you could generate an OTU-based count table using get.oturep:

get.oturep(fasta=XXX, count=XXX, list=XXX, label=0.03)

Which you can then line up with your OTU taxonomies, or regenerate the *.tax.summary file using tax.summary.

Thanks for the response, dwaite.

In case anyone else has similar problems in the future–– I was trying to detect taxa that for some reason weren’t in the silva dataset (using the latest version, v123). I solved this problem by finding the sequences and taxonomy ids from the silva site, and copying and pasting them into the trainset.fasta and trainset.tax files, and rerunning classify.otu.