mothur

How to remove sequences (OTUS) from fasta file based on shared file?

I had a shared file that contained 35000 OTUS. I used remove.rare functions with nseqs parameter equal to 1000, and so I was left with 637 OTUS in that same shared file. How can get the same 637 OTUS but in fasta file? Is there a function that can look at what OTUS I have in shared file and remove all the rest from fasta file?

You can select otus and sequences using the get.otus and get.seqs commands.

mothur > list.otus(shared=yourSharedFile) - list the otuLabels for the 637 OTUs you want
mothur > get.otus(list=yourListFile, accnos=current) - select those OTUs from the list file
mothur > list.seqs(list=current) - list names of sequences in the selected OTUs
mothur > get.seqs(accnos=current, fasta=yourFastaFile) - select the sequences in the selected OTUs from the fasta file

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