Ensembl assembly choice for DNA reference with no combined primary assembly

Question

[AHerik]

Hello, I'm following up on a question that was asked years ago Ensembl assembly choice for RNA-Seq reference mapping

The Bos taurus references on Ensembl are separated by chromosome for the "DNA.primary.assembly", but there is no combined primary assembly for all of the chromosomes. How should one create the combined primary assembly to perform indexing using HISAT2?

Thank you!

Answer 1

[GenoMax]

You can either use the "top level" file of if that is not present then you can cat the individual chromosomes to create a single "genome" file.

If the primary assembly file is not present, that indicates that there are no haplotype/patch regions, and the 'toplevel' file is equivalent.

[AHerik]

Thank you GenoMax ! Is it okay to use the top level file with HISAT2? I've been reading about how haplotype information may not be compatible.

[GenoMax]

See the line from the README file that I added above that you will find here: https://ftp.ensembl.org/pub/release-111/fasta/bos_taurus/dna/README