The fastqc quality control report tells me that there is nextera transposase contamination.
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!
Cutadapt is perfect for contamination like this. After running the cutadapt plugin, you should be able to continue with the normal workflow.