qiime2 feature-classifier classify-sklearn reads' orientation detetion problem

Hi @Natalia_Klimenko , welcome to the forum!

It looks like your reads are in the "same" orientation. Auto-orientation usuaully works well but it looks like it is failing in your case due to the presence of a bad sequence in the database.

The only other time we have seen a similar issue is when reads are in mixed orientations, so that is another possibility, but it looks like instead that "deep sea" group is causing issues.

That sequence is probably either a misannotation in the database or unusually short. See these topics for relevant discussion:

Did you train your own classifier? If so, you might want to check out the RESCRIPt plugin for ways to improve the database before training the classifier (this is what the QIIME 2 pre-trained classifiers use to format the SILVA database and remove low-quality sequences prior to training):

1 Like