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module load fastqc
mkdir raw_Fastqc_Restults
fastqc -o raw_Fastqc_Restults/ -f fastq Lib01_R*.fastq
#scp the resulting .html files to your personal computer to see
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The reads appear to tail off in quality toward the ends. This can be fixed with a program called cutadapt.
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| title | cutadapt and re-check quality |
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| collapse | true |
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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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