How to rename the scaffolds / Chromosomes?

Open nitinShukla1912 opened this issue 4 months ago • 0 comments

Hello,

I used reference based scaffolding, but the issue here is all the names were taken from the reference that I used. I wanted to do NCBI submission of the genome and was thinking to run NCBI EGAPX pipeline for annotation. But somehow I wonder the names of scaffolds or chromosome are from the assembly used for scaffolding.

Am I missing here something?

Oct 02 '25 05:10 nitinShukla1912