Trimming explanation

[jaanckae]

In the trimming step of QuantSeqPoolAnalysis.sh, some parameters remain unclear. Would it be possible to elaborate on them or explain the how and why they are used in the context of this script.

$ cutadapt --quiet -m 20 -O 20 -a "polyA=A{20}" -a "QUALITY=G{20}" -n 2 path/to/output/extracted/sample/R1.fastq.gz | \
> cutadapt --quiet -m 20 -O 3 --nextseq-trim=10 -a "r1adapter=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC;min_overlap=3;max_error_rate=0.100000" - | \
> cutadapt --quiet -m 20 -O 3 -a "r1polyA=A{18}" - | \
> cutadapt --quiet -m 20 -O 20 -g "r1adapter=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC;min_overlap=20" --discard-trimmed -o path/to/output/trimmed/sample/R1.fastq.gz -

There is little to no information in the current manual/readme.

Thanks in advance