The bioBakery help forum

Label for unclassified sequences

Hi all,

With Lefse what is the best way to deal with sequences that are not classified at a given level? E.g. say I have a OTU table with up to genus level information, but some sequences could only be classified up to the family level (e.g. Enterobacteriaceae). Is there a recommended way of naming those unclassified sequences? Should it be any of the versions below?

Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae|_
Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae|Unclassified
Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae|NA

Thanks for any help

Hi Ricardo_Ramiro,

Please try the following pattern?
A|B|C
A|B|unknown
A|unknown|unknown
A|D|E
A|D|unknown

Please replace the unclassified sequences with “unknown”.
Thanks