I have a series of single-end reads from a RAD library of 48 uniquely tagged individuals in fastaq format. The data comes from a small MiSeq run. I want to know the number of unique fragments per individual/barcode, but I'm not sure how to go about getting that number. I'm new to bioinformatics, but I was able to use Stacks to demultiplex the library using the process_radtags function.
Could someone help? Thanks!