Hello everyone. I am a beginner of qiime. When processing a batch of fungal data, I trained my own classifier based on Silva database. But when I run with the classifier, I can only see the level 1 level. I don’t know where the problem is and how to solve it. I need some help. Thank you very much.
Which region are you working on? Silva may contain some fungal 18S data, but
I probably suggest to look at a different database, such as: UNITE (https://unite.ut.ee), especially if you are working with ITS.
Hope it helps
Hello. I work in China. My research is about 18S, so I chose Silva database. I can’t download the unite database, which is a pity.
if you work on 18S, Silva may be of use for you, at least as per its description.
What command did you use to train Silva?
I suggest to check out the Rescript plug in and its tutorial (Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt) for the database preparation.
Hope it helps
Hi @LiyingXie ,
As @llenzi is advising, the issue seems to be poor classification. So you are only seeing level 1 because you only have level 1 classifications. This is usually caused by inappropriately formatted classifiers or the wrong marker.
As you are using 18S, the SILVA full-length classifier should work, and using RESCRIPt (as @llenzi advised, and as I advised on a separate topic) will allow you to format this database appropriately.
Let us know if that fixes this issue!