I was importing sequence data from an IonTorrent sequencer when I ran into an issue where the sequence count is low after Q2 import. When I used Q1’s split_library.py script with default parameters, I got about 2.2 million reads. However, with Q2, I get 890k reads after importing. Is this a Q2 problem?
How are you determining this count? Please share commands, visualizations, etc.
This import command looks great - if you’re missing reads, its because they were lost before importing into QIIME 2. This import step literally just copied your files into a .qza file, no cleanup or qa/qc is applied.
Please share all of the commands or steps you are running, both before importing, and after. Thanks!