>90% unassigned sequences when using feature-classifier classify-sklearn

[SoilRotifer (Mike Robeson)]

HI @hongwei2017,

If you search the forum you'll find that this is likely due to your reads being in a different orientation than the reference database. You can confirm this by looking at the orientation start and stop positions of the query and hit sequence of your BLAST result (remember BLAST will search your query in both directions, i.e. reverse complement, to find a hit). Here is a thread to get you started:

taxonomy db problem

When we see cases in which most of the reads are poorly taxonomically assigned, it is likely that your sequences are not in the same orientation as the reference database. Here are a few threads that may help: When it is not possible to achieve an exact or near-hit to any of the reference sequences, the classifier will return the Lowest Common Ancestor (LCA) taxonomy of similar sequences. -Cheers! -Mike

-MIke