assignment of unclassified groups (summary.tax)

Commands in mothur
1

Hi, I used summary.tax to count the taxa for each of the groups in my data set. I got several taxa designated as unclassified.
Is it possible to have unclassified_bacteria or unclassified_Pseudomonadaceae instead of this? If I am right it could be derived from the preceding tax level based on the rankID?
Thanks Andreas

2

If you look at the outline in the summary file, you’ll see that the preceding level will have the taxonomic level.

3

Yes, I understand that I can manually add the respective information, eg.:

  • taxlevel rankID taxon
    …
    5 0.1.2.1.2.14 Micrococcaceae
    …
    6 0.1.2.1.2.14.3 unclassified

change to:

  • 6 0.1.2.1.2.14.3 unclassified_Micrococcaceae

My question is, if there is a possibility to perform it automatically using Mothur.
Cheers Andreas

4

I’ll add it to the future features list - thanks for the suggestion

5

Hi,

I see that in the release Mother v.1.37.0 you added as reported below the assignment for unclassified groups with the summmary.tax, classify.otu and classify.seq.

Is there a command to have still only the “unclassified” label without the assignment, or shall I use older version of Mothur to do it?

Thanks in advance and best regards,
Edoardo Puglisi

6

Does it break other scripts? We felt like this was more informative than just a blank “unclassified”

Pat