Remove OTUs using an input list

Commands in mothur
1

Dear all

I need to remove a few OTUs (appx 100) from my list and shared files (e.g Otu00110, Otu01234, Otu02235 etc etc)

I can see that there is the “remove.otus” command and I can see that I can use an input file/list of the OTUs that I would like to remove but I am not sure what format the input list should have and how do I specify the input in the command?

any help would be greatly appreciated as I do not want to do it manually… :?


cheers P
2

If you put the sequence names into a file (e.g. remove.accnos) with each sequence name on a separate line, you can then do

remove.seqs(accnos=remove.accnos, fasta=allseqs.fasta)

Pat