Loosing reads when demultiplexing with cutadapt

Yeah, something is still wrong up here. After flipping the barcodes, the 8 samples that demultiplexed all have acacacac in the seq_barcode_F column. (or perhaps in the seq_barcode_R column if that's how you flipped it)

This gives me less confidence that either way is correct :scream_cat:

Was the sequencing center able to successfully demultiplex your samples? It's possible we are still missing something, but if they are using a custom protocol, they may have a way to solve this problem. If so, they could send you pre-split results with each sample in a pair of fastq files, and we could take it from there!