remove.otus and remove.otulabels

Commands in mothur
1

Hi,

I am trying to remove OTUs from a taxonomy file to make it ‘match’ a sub.sampled shared file.
I used these commands:
list.otulabels(shared=su18.opti_mcc.0.03.subsample.shared)
remove.otulabels(accnos=su18.opti_mcc.0.03.subsample.0.03.otulabels, constaxonomy=su18.cons.taxonomy)

The way I read the remove.otus and remove.otulabels wikipages this should remove OTUs NOT in the accnos file (i.e. su18.opti_mcc.0.03.subsample.0.03.otulabels).

However, it instead removes all the OTUs that are IN in the su18.opti_mcc.0.03.subsample.0.03.otulabels file.
I also tried remove.otus and got the same result.


mothur > list.otulabels(shared=su18.opti_mcc.0.03.subsample.shared)

0.03

Output File Names:
su18.opti_mcc.0.03.subsample.0.03.otulabels


mothur > remove.otulabels(accnos=su18.opti_mcc.0.03.subsample.0.03.otulabels, constaxonomy=su18.cons.taxonomy)

Removed 9542 otus from your constaxonomy file.

Output File Names:
su18.cons.pick.taxonomy


mothur >
2

The remove commands remove the items listed in the accnos file. The get commands select the items listed in the accnos file. Can you try this:

mothur > list.otulabels(shared=su18.opti_mcc.0.03.subsample.shared)
mothur > get.otulabels(accnos=su18.opti_mcc.0.03.subsample.0.03.otulabels, constaxonomy=su18.cons.taxonomy)

1 Like
3

Thanks! That worked.
Camilla