remove.lineage

Commands in mothur
1

Hi,
I used the classify.seqs with the silva.archaea database on a my sequences and tried to remove unclassifed sequences at the kingdom level (i.e. sequences that are not archaea). The problem is that when I put unclassified in taxon:

remove.lineage(fasta=arch.trim.contigs.good.unique.good.filter.unique.precluster.pick.abund.fasta, count=arch.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.abund.count_table, taxonomy=arch.trim.contigs.good.unique.good.filter.unique.precluster.pick.abund.silva.wang.taxonomy, taxon=unclassified)

the remove.lineage function removed all unclassified sequences (due to poor taxonomic classification in archaea, most sequences are unclassified after the phylum or class level), not only at the kingdom level. Is there a way to remove lineage based on rank.ID?
Thank in advance
JC

2

Try using taxon=unknown. If a sequence does not classify at the kingdom level it will come back as “unknown”.

Pat

3

My bad, my explanation was not very good. By choosing the Silva archaea database, I assumed that all my sequences were archaea but some were unclassified at the phylum level. to get rid of them the good command was taxon=Archaea;unclassified. I’ll import them in arb just be sure there are not archaea.
Thank’s for your reply

4

Hi
How can I know which sequences were removed because they were identified as contaminants and if they were chloroplasts, archaea, etc? with the summary I only can know that there were some seqs removed but that´s all.
Thanks!

5

Please start a new thread so that we keep the content of each tread homogeneous.

Pat