mothur

Classify.seqs-- How to get the names of the reference sequence

#1

hi Pat
The classify.seqs command usually returns the taxonomy information.
How can I get the sequence names of the reference sequence in the template？

For example
the taxonomy；

172163 k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__;g__;s__

How can I return the “172163” to my submit sequences not only the “k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__;g__;s__”

THANKS!

#2

That’s a greengenes accession number. You could probably use get.seqs to pull out the actual sequence and see if there’s other information in the sequence header.

Pat

#3

Thank you for your reply.
I may not have expressed my problem clearly.
When using “classify.seqs” command to classify my own sequence, the file usually returned is “**** .summary” and “.taxonomy”
In “.taxonomy”, the result is:
xg1.3.186974 (my seqs name) k__Bacteria(100); p__Gemmatimonadetes(100); c__Gemmatimonadetes(100); o__Ellin5290(85); f__(85); g__(85);

I want the result returned in the “****.taxonomy” file to be
the accesson ID replaces the specific taxonomy information.
such as ：
xg1.3.186974 (my seqs name) accesson id in greengenes

Can this need be realized directly? Can it be realized by other indirect means?

#4

That’s not how the Bayesian classifier works. The classifier gives you a confidence score that a sequence has a specific classification. The problem is that there are often many things that are just as good a match and it would be biased to claim one is a better match over another. That is certainly possible using one of the other methods in classify.seqs, but I do not recommend them.

#5

Thank you very much ！