How do I know whether my 16S metagenomics data files have the barcodes and primers removed or not by the sequencing center? Is there any plugin that I can run prior to using cutadapt to figure this out?
My data was generated on a MiSeq reporter and I have demultiplexed paired-end reads.
The best way to find out is to talk to your sequencing center! They can tell you specifically what happened with your data, and it’s always good to be friends.
Thanks, Justine I did contact them and haven’t heard back yet. So I was wondering whether there’s any other way to do this.
You could try looking at the alignment, but TBH, I think your absolute best solution will be talking with them. One of the best things I have ever done for my bioinformatics is to make friends with the people doing the lab work and to regularly remind them how awesome they are?