FORUMCategory: SequencingHow to get rid of the right adapters?
jstafford asked 2 years ago

Hi all – question: I ran FastQC on some samples and it’s reporting a lot of adapter contamination near the end of my reads. I’ve found some tools like cutadapt and trimmomatic, but they all want an adapter sequence to trim? How do I figure out what adapter sequence I need to trim?
If it helps, FastQC is just reporting things as “Illumina Universal Adapter”.

1 Answers
Best Answer
zhibin Staff answered 2 years ago

You can try to use the first 13 bp of Illumina standard adapters (‘AGATCGGAAGAGC’). This is the common sequence of both TruSeq Universal Adapter and TruSeq Indexed Adapter.

jstafford replied 2 years ago

That works, ran that through cutadapt and all the adapters are gone now!