Reference Genome dna, rm or sm??

Question

[Akash D]

I found three types of Toplevel genome i.e dna, rm and sm. By now I know the difference but which to use for your for RNA-Seq analysis?

Any help would be appreciated

Thank you Akash

Answer 1

[GenoMax]

See Why is human genome FASTA file on GENCODE much smaller than that on ENSEMBL?

Use primary unmasked genome. Do not use Toplevel file.

[Akash D]

Thank you GenoMax