Hi qiime2 forum, I am attempting to analyze a dataset generated from fungal ITS sequences, and have run into similar issues as the following two threads, however haven't been able to solve my problem with the advice therein: [image] Training classifier for ITS classification User S…

Great question! I would also like to hear what the Qiime devs recommend as supporting many databases is important. For reference, here is the current documentation on retraining the feature classifier .

Hi @Hillary_Smith , Thanks for posting! And many thanks for checking out the other forum posts related to this issue first. I have a few questions to get started troubleshooting: What primers are you using? What is the length of the sequences that you are classifying? What types of samples are you…

Hi Nicholas, Thanks for the quick reply!! I am using primers ITS1F (forward; Gardes and Bruns 1993) and ITS4 (reverse; White et al 1990) following this protocol. The sequences are Illumina HiSeq, so 2x300bp. The samples were isolated from 3 different species of Acropora corals. I tried c…

Hi @Hillary_Smith , It sounds like your classifier is working fine (and we/other qiime2 users have used the UNITE classifier quite a bit so there should not be compatibility issues). So the bad news is this is not an easy fix, but the good news is that you can try to extract the useful sequences and…

Hi @Nicholas_Bokulich - Thanks so much for your advice. I realized I had done something stupid in an earlier step, and figure it might help people if I share it here. We used 2x300bp paired end technology, so I thought naturally I should join the paired-end reads. However, due to variation in the …

Thanks for the update, @Hillary_Smith !

[image] Nicholas_Bokulich: use filter-features to include only sequences that align to the UNITE database within some % identity (maybe 90%? 80%? Hi @Nicholas_Bokulich - Trying to follow your recommended steps above, and can't figure out how to filter features based on % identity match to th…

Hi @Hillary_Smith , You can use exclude-seqs to filter out features based on their % identity. (sorry — I linked to the correct tutorial above, but gave the wrong method name. filter-features would be used to subsequently remove these features from your feature table). You can use the perc-identity …