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Unclassified vs "not classified" #41
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Hi, |
Hi @mihinduk and @Finesim97, Yes you are right! Sometimes a contig is classified at a higher level than superkingdom, in which case CAT considers it classified but you won't find any classification on the official ranks. The logic for this behaviour is that giving names to the lineage at official ranks is a post-classification step, and CAT is agnostic as to which level you want a classification to be made before something is called unclassified. Hope this helps! Best wishes, Bastiaan |
This makes sense. Thank you so much for your quick reply. Kathie |
Hi,
I am trying to use CAT to annotate contigs derived from Illumina sequencing and assembled by Megahit. My understanding is that "Not classified" means that something prevented the classification of the contig, like "no hits to database", "hits not found in taxonomy files" or "no ORFs found". I have a number of "Classified" in the out.CAT.alignment.diamond file that have alignment scores of > 0.5 at one or two levels to a NCBI protein ID but - although that protein ID has taxonomy, they are labeled "not classified" at all levels.
Why are these in 2 separate bins, instead of the 2nd instance being a subset of the first "unable to be confidently classified"? Am I misunderstanding these results?
Thank you for your help,
Kathie Mihindukulasuriya
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