I am using ipyrad for my ddRAD data analysis. Your tutorials are excellent and easy to follow. For my project, I pooled samples from two different species in one sequencing run. Each sample is individually barcoded. I would like to analyze the data from different species separately. Please help me. Thank you - Nirsha
@rfolkert ipyrad doesn't take into account base quality when matching barcodes during demultiplexing. Are you worried about reads being misassigned? In practice this is very uncommon, so i wouldn't worry too much about qc'ing prior to demux.
@isaacovercast thanks for your quick reply! I am just being a bit cautious, allthough my barcodes are sequenced before the restriction site, the base-quality at the restriction site looks quit bad(PE ddRAD), therefore I was a bit worried.