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"No samples found with any adapter contamination > 0.1%" Is adapter-trimming still necessary?

Hello, everyone,

After running fastqc on my raw data, I realized that the adapters are already removed (>%0.1). Would adapter-trimming in this case still improve the sequence quality? Or I can just skip it and only apply the quality-trimming?

Thank you. :)

rna-seq rna-seq next-gen
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updated by GenoMax GenoMax • written by Jay-Run • Jay-Run

1 answer

Most aligners will soft-clip sequences that don't match a reference (e.g. adapters) so it is ok to omit scanning/trimming as long as you have a good reference to align to. If you are doing any de novo assembly work then you should scan/trim your sequences, no matter what FastQC says, to make sure all extraneous sequence bases are removed prior to assembly.

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written by GenoMax GenoMax

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