itsxpress does not extract sequences where ITSx does

[Nicholas_Bokulich]

@Adam_Rivers

Your idea of simple reversing the input strands (or importing them reversed is an interesting one, that we had considered back in December. I would need to think about the parsing of this a bit more because when you reverse the forward and the reverse reads the positions we cut from based on the HMM coordinates change.

What about just swapping the forward and reverse reads at importing, as I proposed above — I do not see how this is functionally different from importing reads in the correct orientation, except that (I think) the reads would be forward complement to what standard ITS primers yield:

Is that right? Does itsxpress not support forward complement? So the reads need to be in the correct orientation and on the correct strand?

@Adam_Rivers

Would you be willing to share some example data for me to work with? Maybe 2 samples with 5000 thousand read pairs?

A quicker test dataset may be to use Taylor's own mock community data, which are used in this tutorial:

Fungal ITS analysis tutorial

Fungal ITS analysis, mock communities, and more fun NOTE: This tutorial was written in a QIIME 2 2018.11 environment. It is not guaranteed to work with earlier or later versions of QIIME 2. This tutorial was compiled as a working exercise for a QIIME 2 workshop in December 2018, and does not represent the only possible fungal ITS workflow with QIIME 2, or even a benchmarked protocol recommendation. See other tutorials, e.g., the q2-itsxpress tutorial for other fungal ITS analysis options in QII…