Hi @gregcaporaso,
Thank you!
Sure, please see the manifest file attached. For some sequencing files on the manifest file, I had to modify the fastq file (remove adapters, trim) while others were okay so I lefted as zipped.
Yes, there were problems identified by FastQC and I used TrimGalore! to resolve them.
I think I found the major issue though. When I used: head -n 2808240 1868616S.fastq | tail -n 20 (as you suggested) in Linux, I could not see any issues with the sequences and their respective quality scores. When I used Microsoft visual studio code to review the same line in the entire fastq file, I noticed some sequences do not have any quality scores. (see image below)
It makes sense I was able to produce the demux-paired.qza if sequences were present but that the qiime tool's validation of the demux-paired.qza failed since quality scores were missing. Thank you for the alternative suggestions. I asked the sequencing facility to amend this issue before working on the analysis for now, but let me know if you think I should still try to use > qiime dada2 denoise-paired before resolving the Q-score issues.
OmniActive_manifest_file.txt (4.8 KB)