mothur

Remove.lineage() to filter unclassified OTUs at specific taxonomic levels

I’m sure I’m missing something obvious here, but I have not found an answer that works for my specific situation. I am wanting to remove OTUs that are unclassified at anything above a family level.

I have used this code, but I am not sure how to get the filter down to a finer resolution without knowing specifically which phyla, orders, or families to put into the code:

remove.lineage(fasta=seqs.good.unique.pick.txt, count=seqs.good.pick.count_table, taxonomy=seqs.good.unique.pick.2019_taxonomy.wang.taxonomy, taxon=Fungi_unclassified-unclassified_Fungi)

Again, I’m probably just being dense about this, but I would love to figure this out.

Thanks!

Hi there,

Unfortunately, there isn’t an easy way to do what you’re asking purely in mothur. Here’s what I would do…

If you’re using Mac/Linux, you can run this command to get the listing of sequences that have a taxonomy that includes “unclassified”…

$ grep "unclassified" stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.taxonomy | cut -f 1 > unclassified.accnos

This creates a file called unclassified.accnos that has the listing of sequences that are unclassified. You can then use this within the remove.seqs command from within mothur along with your current fasta, count_table, and taxonomy files (i.e. the ones parallel to stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.taxonomy used in the example above)

mothur > remove.seqs(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.count_table, taxonomy=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.taxonomy, accnos=unclassified.accnos)

Pat

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