I am a novice Qiime2 user and I hope my questions here are not too silly.
The current version I’m using is: qiime2-2020.2
I installed it using conda environment on my Linux.
I have a question with the trimming of 16S sequence based on the quality of reads (currently trying Q20, Q25 and Q30). I had noticed that the trimming of reads was done after all the sequence files were imported, i.e. if the experiment was completed with 18 samples, all the 18 samples were imported at once and the quality trimming was done in the same settings for all sample right after (as in an assumption was made that all the 18 samples have the same exact quality, though, please correct me if I’m wrong).
For my 16S data, I noticed that each sample has different sequence length to its quality. I would like to opt for specific trimming for each sample individually. However, after the trimming of each samples using dada2, I had noticed that the output files is no longer a .fastq file to proceed with qiime analysis. So how do I import all the data? or maybe Qiime2 has another pipeline to tackle this issue?
I would like to apologize one more time if my questions are silly etc. I am new to Qiime2 and still learning the ways to analyze metagenomic data. I also would like to thank you in advance for your time and effort to help.