about plotQualityProfile and derepFastq function

[dstrgcv]

Q1: truncLen parameter in filterAndTrim function is determined by plotQualityProfile. however, I think its objective to see the green line to select the values. is there any standard such as the threshold value of quality score to select the best truncLen parameter?

Q2: I see the current tutorial omitted the derepFastq procedure, but the previous one have derepFastq ofter filterAndTrim

[benjjneb]

Q2: I see the current tutorial omitted the derepFastq procedure, but the previous one have derepFastq ofter filterAndTrim

derepFastq now happens "on the fly" within the learnErrors and dada functions. This reduces memory requirements dramatically on large datasets, as only one sample needs to be loaded into memory at a time instead of all at once as in the previous tutorial version.

Q1: truncLen parameter in filterAndTrim function is determined by plotQualityProfile. however, I think its objective to see the green line to select the values. is there any standard such as the threshold value of quality score to select the best truncLen parameter?

I wouldn't worry too much about trying to find the optimum truncation length. The goal is to cut off the tails of sequences after a "quality crash", as is often seen towards the end of Illumina reverse reads, while maintaining enough overlap between paired reads to allow them to merge after truncation.