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?
I would trim your reads to a consistent length, even if its past where you. have the low quality sequences (Have you checked your full read lengths? That may be a better guide than quality!)
Quality filtering and denosing should help take care of the low quality reads for you, so I would not worry about trimming. However, it’s worth checking the demultiplexing summary after quality filtering and the denosing stats to see where you’re losing reads.
