Cordial greeting. I have demultiplexed merged pair-end reads, it means I have only one fastq file for each sample (I got them like that from the sequencing center).
Then I got the output visualization file and I obtained next figure into qiime2 visualization page.
I will use Deblur denoise for my samples (as they are merged reads).
I have two questions
how determine the --p-trim-length parameter from the next figure, it should be 340? (same length for all samples),
how can I trim those samples between 150 and 200 sequence base (x axis in the figure) which have a quality score below 25?
Thakns a lot !!