ITSexpress and ITS data upstream analysis

It's good to hear from you again. Sounds like your Dockerized Galaxy deployment of Qiime2 is working well.

I'm not an expert on ITSxpress, but it looks like something went very wrong. Not only are all by 17 of your reads missing, the whole reverse read is gone! :exploding_head:

It wonder if passing a different region other than --p-region ITS2 would help. Are you sure these reads came from ITS2?


Your dada2 stats look pretty good!

That's tutorial is the most up to date that I can find too. There is also documentation on the plugin page and on Github.

Here are direct links to the Unite database files for version 8.3:

# 8.3	2021-05-10	Fungi	14 097	44 343	Current	https://doi.org/10.15156/BIO/1264708
wget -qO- https://files.plutof.ut.ee/public/orig/C5/54/C5547B97AAA979E45F79DC4C8C4B12113389343D7588716B5AD330F8BDB300C9.tgz | tar xz -C downloads --strip-components 2 # sh_qiime_release_10.05.2021       # normal

# 8.3	2021-05-10	Fungi	14 097	83 993	Current	https://doi.org/10.15156/BIO/1264763
wget -qO- https://files.plutof.ut.ee/public/orig/B3/05/B3054DF783AC61A0C3BD0FDEB0516EC394934809AAE43CA0F3081C0A184FAA39.tgz | tar xz -C downloads --strip-components 2 # sh_qiime_release_s_10.05.2021     # add s for 97% singletons

# 8.3	2021-05-10	All eukaryotes	14 237	96 423	Current	https://doi.org/10.15156/BIO/1264819
wget -qO- https://files.plutof.ut.ee/public/orig/48/29/4829D91F763E20F0F4376A60AA53FC9FBE6029A7D1BDC1B45347DD64EDE5D560.tgz | tar xz -C downloads --strip-components 2 # sh_qiime_release_all_10.05.2021   # add all for Euks

# 8.3	2021-05-10	All eukaryotes	14 237	190 888	Current	https://doi.org/10.15156/BIO/1264861
wget -qO- https://files.plutof.ut.ee/public/orig/1D/31/1D31FA3A308BDC2FB2750D62C0AA40C5058C15405A3CC5C626CC3A3F5E3903ED.tgz | tar xz -C downloads --strip-components 2 # sh_qiime_release_s_all_10.05.2021 # and s and all for 97% Euks singletons

I have pre-built versions of the Unite classifiers available over here, if you would like to give them a try.