Dear all, I have a question about the use of trimmomatic. I have used the Illuminaclip step (The one which removes adapters) in trimmomatic even if the QC tool indicated no adapter contamination whatsoever. Not sure if this is an issue or not. Indeed, I wonder if using the Illuminaclip for removing Nextera or Truseq3/2 adapters, this unnecessary step would have removed fragments inside the read – should the tool not find the adapter sequence at the beginning of the read. I imagine the clipping steps are highly specific for the chosen adapters, so no harms done to the fastq files, hopefully?