I would appreciate some advice. I have generated SNP sequences using DiscsoSNP-RAD and figured out a pipeline to import the data into STRUCTURE to look at population structures. I am trying to perform a similar experiment as Gauthier et al. did in their paper DiscoSnp-RAD: de novo detection of small variants for population genomics. The fasta file produces SNP sequences of upper and lower paths as demonstrated below:
My question is, should I use only one of the paths or both of the paths for STRUCTURE analysis? If one, which path would be best? I appreciate any feedback!
Thank you in advance