scaffold in reference genome

Question

[ft.mastouri]

I downloaded the reference genome for glycine max from JGI. It contains the 20 chromosomes and some 2000 scaffolds. My question is if scaffolds are needed or should be removed. Should I remove them manually or else how can i get chromosomes only?

Answer 1

[colindaven]

The scaffolds are needed, they are likely parts of the reference genome which could not yet in this assembly build be confidently assigned to chromosomes. This is typical of repeat containing scaffolds. They are likely to be small and not gene rich, but excluding them would cause short reads which should map to them to be forced to map to the chromosomes and cause problemes downstream, such as false SNPs etc.