nextera transposase contamination

General Discussion
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Dear all,
The fastqc quality control report tells me that there is nextera transposase contamination.

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part of nextera transposase sequences are inserted into the reads.
nextera transposase adapter：F:TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG R：GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG
Anyone knows how to deal with nextera transposase contamination? Is cutadapt ok?
What would be an acceptable level of contamination?
Thank you very much!

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Cutadapt is perfect for contamination like this. After running the cutadapt plugin, you should be able to continue with the normal workflow.

Colin

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