Dear colleagues, I am still new to QIIME2 and I am following the online tutorials. I would like to denoise my joined paired-end sequences but I am struggling to understand how to figure out the trim-length value when I run this command:
qiime deblur denoise-16S
Following the tutorial here, Alternative methods of read-joining in QIIME 2 — QIIME 2 2021.2.0 documentation, this value has to be determined using the quality plot generated from Vsearch (see here, QIIME 2 View) but I am failing to grasp how the 250 was determined. In other words, I am failing to interpret the plot to determine the length of the sequences.
When I tried to run my own data, I figured out the length may be 290 (of which I think I misinterpreted the quality plot) but when I tried to view the feature table using the following command, I got zeros and nans meaning there was nothing in the table:
qiime feature-table summarize
What could be the problem?