removing OTU representative sequences (.rep.fasta) based on taxonomy (using remove.lineage)

Aloha Sarah, Pat et al.

We wanted to use remove.lineage to remove putative chloroplasts from our analyses after OTU generation and the selection of consensus or representative sequences for each OTU. We found that we could use this command nicely on .list and .shared files and even .cons.taxonomy files, but were unable to remove sequences from the .rep.fasta (and though we didn’t test it, probably also anything generated from the consensus sequence commands).

Would it be reasonable to allow a repfasta input to remove.lineage and similar commands?


I assume the remove.lineage command you ran looked something like:

remove.lineage(constaxonomy=yourConsensusTaxonomiesForEachOTU, list=yourListFile, shared=yourSharedFile, taxon=yourContaminants) - removes contaminated OTUs from your list and shared files.

To get the OTU representatives for these new contaminant free OTUs, you can do the following:

mothur > list.seqs(list=yourContamiantFreeListFile)
mothur > get.seqs(fasta=*.rep.fasta, accnos=current) - selects the reps from each “good” otu