Is it okay to use dna.toplevel file for alignment if primary assembly file is not available?

Question

[pubsurfted]

I cannot fine the primary assembly file for glycine max on ensembl plants. Can I use dna.top.level file or should i just stick to the sm files? I have read somewhere that "If the primary assembly file is not present, that indicates that there are no haplotype/patch regions, and the 'toplevel' file is equivalent.".

Answer 1

[GenoMax]

Yes you can use the top level file as indicated in help readme file.