I am doing qiime2 analysis on Phytophthora samples but it seems that there is no ITS database for Phytophthora sequences. I checked UNITE database but it is just for Fungal ITS. Also in the SILVA database, the sequences are for 18S and 28S markers and there is no ITS database here.
I got a full list of ITS sequences for Phytophthora (as attached) but it should be qiime-compatible while it is not.
Any comment and help will be highly appreciated!
Best Wishesdatabase.txt (222.3 KB)
Check out some of the compatible datasets, such as greengenes or UNITE to see what the correct format is. If you get your data into that same format, you will be able to use this custom database.
Sequences: fasta format
>AF271224.1 CCACACCTAAAAACACCCTTCCAC... >AF271225.1 CCACACTTTAAAAAACTGTCCACG...
Taxonomy: tab-delimited format
AF271224.1<tab>Pythium vexans AF271225.1<tab>Pythium ultimum
Hint: if you want to learn some bash programming to help make the taxonomy file, check out “grep” and “sed”…
Thank you my friend for your kindly advise!
I will try to do it as you mentioned. But i think the taxonomy file must be more complicated than you said. I mean, all taxonomy levels for each sequence should be given, not just the genus and species name.
Anyway, thank you again!
Indeed, creating a taxonomy file (and databases more generally) is a very complicated task.
You do not actually need to provide all taxonomic levels, necessarily. Genus and species name is okay as long as you are happy doing a top-hit match instead of, e.g., looking for a consensus taxonomy. So you can use
feature-classifier classify-sklearn --p-confidence -1 and the classifier will just find the top match. Another option is to just provide genus and species names:
AF271224.1<tab>Pythium; Pythium vexans AF271225.1<tab>Pythium; Pythium ultimum
This should work with any of the methods in QIIME 2, but you will get an “unclassified” result if a sequence cannot be assigned to at least genus level.
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