filter shared by taxonomy

Commands in mothur
1

I’d like to generate otu matrices of specific phyla. How could I do this? I’ve classified the otu’s so have the taxonomy file and the shared file.

2

at this poitn the easiest way would be to run get.linage for the groups you want, dist.seqs, cluter, make.shared

3

oh bummer. a few of my phyla are huge (100k preclustered seqs) redoing the distance matrix and clustering on that phyla, which naturally would be my first target, would take a week or so.

4

Thanks for the feature request. In version 1.31.0 you will be able to do the following:

mothur > classify.otu(list=final.an.list, taxonomy=final.taxonomy, name=final.names) - classify OTUs
mothur > get.lineage(constaxonomy=final.an.0.03.cons.taxonomy, shared=final.an.shared, label=0.03, taxon=‘Bacteria;Firmicutes;’) - select OTUs that classified to Bacteria;Firmicutes;.

Output File Names:
final.an.0.03.cons.pick.taxonomy
final.an.0.03.pick.shared


or

mothur > classify.otu(list=final.an.list, taxonomy=final.taxonomy, name=final.names) - classify OTUs
mothur > get.lineage(constaxonomy=final.an.0.03.cons.taxonomy, list=final.an.list, label=0.03, taxon=‘Bacteria;Firmicutes;’) - select OTUs that classified to Bacteria;Firmicutes;.

Output File Names:
final.an.0.03.cons.pick.taxonomy
final.an.0.03.pick.list

5

sweet, thanks Sarah

6

Hi, very nice - works fine.
Can I also extract a fasta file?
Thanks

7

To get the fasta file containing the sequences in the final.an.0.03.pick.list file, try running:

list.seqs(list=final.an.0.03.pick.list)
get.seqs(fasta=yourFastaFile, name=yourNameFile)

You may also want to include your group file:

list.seqs(list=final.an.0.03.pick.list)
get.seqs(fasta=yourFastaFile, name=yourNameFile, group=yourGroupFile)

8

works just fine! Thanks a lot!