About the selection of reference genome

Open cnxiaobo94 opened this issue 3 years ago • 1 comments

Hi, dear friends. I have a question on processing rawdata. When I made PCA or Dst. analyses, I need to take a outgroup species as reference genome for processing rawdata. My question is that whether the existing genomes of the analyzed species can be used as reference genomes to processing sequence data for PSMC analysis?

Apr 14 '23 12:04 cnxiaobo94

Depends on how taxonomically distant the reference is from your data. You may find this paper helpful from Prasad et al, 2021

Apr 15 '23 00:04 plubbe