Low count during import of single-ended sequences

[emmzee]

Hi everyone!

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?

Here is the script I used:

qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path manifest.csv --output-path imported_seqs.qza --input-format SingleEndFastqManifestPhred33

[thermokarst]

@emmzee

Hi everyone!

Hello!

@emmzee

However, with Q2, I get 890k reads after importing

How are you determining this count? Please share commands, visualizations, etc.

@emmzee

Here is the script I used:

qiime tools import --type ‘SampleData[SequencesWithQuality]’ --input-path manifest.csv --output-path imported_seqs.qza --input-format SingleEndFastqManifestPhred33

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!