I used pre-trained classifiers (Greengenes 2022.10 and Silva 138SSURef NR99 full-length) provided in QIIME2 data resources for taxonomic classification. When I compare the taxonomic assignments with the taxonomy of the best BLAST hit for the feature IDs that are not assigned to Level 7 (Species) by QIIME2, I managed to obtain the Species name. How do I link BLAST result (i.e. Species name) to QIIME2 feature IDs so that my taxa bar plot contains the name of the Species?
Thank you for your help.
Unfortunately there is not an easy answer here and ultimately it may turn out to be the case that there simply is not enough information in your reads to make assignments to the species level However, there are some things you can do to improve your results, such as training your own classifier; for those, checkout this post and accompanying responses!
Hopefully it will help you get results you are looking for, or at least provide some good background for further refining them!
Thank you for your reply!
I managed to train my own classifier using Silva. However, when I attempted to do the same using Greengenes2, I encountered problem in downloading the necessary files from the FTP server. I cannot:
- open the FTP in my browser, or
- download via wget (with or without --no-check-certificate, using https returns "Unable to establish SSL connection" while using http results in "Read error (Connection reset by peer) in headers.")
May I know how to solve this?
Have you been able to resolve this issue? It sounds like it may have been some sort of temporary networking problem. If not, we're happy to troubleshoot further.
Yes, I can now access the databases. It is now all good. Thank you for following up!
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