Thank you, Nicholas!
I've managed to get the quality scores for this data, and the quality plot looks now as follows:
And now when I run dada2, there is a new error:
There were some problems with the command:
(1/3?) no such option: --p-trim-left-f Did you mean --p-trim-left?
(2/3?) no such option: --p-trunc-len-f Did you mean --p-trunc-len?
(3/3?) no such option: --p-max-ee-f Did you mean --p-max-ee?
I've seen a similar problem on forum, but it looks like the guy simply mixed up commands
qiime dada2 denoise-paired
and
qiime dada2 denoise-single
In my case, I have only forward read and use the correct command which gives me the error above.
Here is my code:
qiime dada2 denoise-single
--i-demultiplexed-seqs single-end-demux.qza
--p-trim-left-f 18
--p-trunc-len-f 158
--p-max-ee-f 2
--p-trunc-q 2
--p-n-threads 0
--output-dir DADA2_denoising_output
--verbose
Do you have any idea about that?
Thank you for your help, really appreciate it!