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: https://avikarn.com/2019-04-21-AmpSeq/
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.