Get OTUs from list of seqs

Commands in mothur
1

Hi all!

I have a list of sequences and would like to get the OTUs they belong to. Is there a better way than using bin.seqs? That will give the information, but I’d prefer a table output without the actual sequences, and ideally with the OTUs printed in the same way as in the shared files.

Cheers,

Till

2

You could try:

get.seqs(list=yourListFile, accnos=listOfSeqsYouWant, group=yourGroupFIle)
make.shared(list=current, group=current)

Note: If the get.seqs command does not select any sequences from an OTU, it will be eliminated from the list file. This will cause the OTULabels in the shared file to change when compared to the shared file made from the complete dataset.