This tutorial video is my attempt to introduce the basics of the AmpSeq data analyis in Marker Assisted Selection . For general information on technology behind AmpSeq please read one of my previous blog post on it at this link:

A few suggestions before you analyze your AmpSeq data for MAS:

  • Remove markers with unknown, uninformative or with a lot of missing data.
  • Unvalidated desirable alleles are recommended to be validated prior to impleting those markers in production phase of the analysis
  • Please keep an eye on markers with low read counts, especially that are homozygous, because it could be a heterozygous undercalling issue.
  • Minor suggestion, while color highlighting in MS Excel using Find and Replace function, please double check the highlighted cells. Because sometimes for example while trying to highlight allele `1`, undesirable allele `94/94:1` gets highlighted - please watch out for those!
  • Adding the "Keep/Discard" column is optional. However, I prefer having it because its very helpful in making selection on multiple traits/loci in a common genetic background.

Thank you for watching this tutorial. If you have any questions or comments, please let me know.

Happy AmpSeq-ing !

Image credits: I would like to gratefully thank Mike Colizzi for sharing images used in the tutorial video.