report on all seqs

Is there a way to get MOTHUR to report every sequence, it’s OTU, and classification (including the non-unique sequences). I want to get it after the precluster has been run. I tried to do this by not using the unique.seqs command but precluster automatically runs it.

My goal here is to determine what percentage of the total number of sequences (without subsampling) fell into each OTU for each treatment, after everything has been cleaned up and preclustered.

Thank you!

The shared file will give you the abundance breakdown by group. If you run get.relabund(shared=yourSharedFile), you will get the relative abundance of each OTU for each group. OTUXsampleARelativeAbundance = OTUXsampleAAbundance / totalNumSeqsInSampleA. Or you can run get.relabund(shared=yourSharedFile, method=totalotu) OTUXsampleARelativeAbundance = OTUXsampleAAbundance / totalNumSeqsOTUX. For the classifcation of each otu, classify.otu(list=yourListFile, taxonomy=yourTaxonomyFile, name=yourNameFile), or for a classification persample classify.otu(list=yourListFile, taxonomy=yourTaxonomyFile, name=yourNameFile, group=yourGroupFile, persample=t). Is that what you are looking for?

Yes! That’s it. I had sort of cobbled things together by fishing through all the files the first time, which took quite a while. Figured there had to be a command for it.
Thank you!