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cutAdapt sequences

What are the sequences which should be given to cutAdapt in order to trim the standard Illumina adapters?

Jonathan Barlev

1 Answer

cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT \
-o $file"_R1.cutadapt.fastq.gz" -p $file"_R2.cutadapt.fastq.gz" \
-m 40 \
$file"_R1_001.fastq.gz" $file"_R2_001.fastq.gz"

Jonathan Barlev

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