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#run cutadapt without any adapter sequences to cut, but with a PHRED quality cutoff of 30
#(a PHRED score of 30 indicates an expected error rate of 1/1000)
cutadapt --pair-filter=any -q 30 -o Lib01_R1_qced.fastq -p Lib01_R2_qced.fastq Lib01_R1.fastq Lib01_R2.fastq
#now rerun FastQC to see how it worked
mkdir qced_Fastqc_Restults
fastqc -o qced_Fastqc_Restults/ -f fastq Lib01_R*_qced.fastq
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