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!

  • $\begingroup$ Do you mean the barcode in the FASTQ header? $\endgroup$ – FoldedChromatin Aug 11 '16 at 8:33

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