Q2-itsxpress param help


(Manuel Ponce Alonso) #1

Hi Adam, thanks for developing that plugin. I have a doubt regarding the --p-taxa parameter. You have set it to “F” in the example, but I don’t understand which I should use (ALL?). I´m processing ITS1 reads from clinical samples, sequenced by Miseq (2x300pb).

Thanks!


Q2-ITSxpress: A tutorial on a QIIME 2 plugin to trim ITS sequences
(Adam Rivers) #2

Generally the F parameter should be used unless you are targeting something specific like a mocrosporidian or something even more divergent like a marine diatom. Running ALL will not hurt anything but it will take much longer to process since more HMM models are searched. You can always run 1 sample both ways and compare the results.


(Manuel Ponce Alonso) #3

OK, then I will run my sequences under the F mode. Thanks Adam!