I have RNA-seq data from the BALB/c mouse strain.
Looking for the reference genome on Ensembl, I found that, the most recent version, GRCm38 was build using the C57BL/6J strain.
I suppose that, the PATCH files contains haplotypes and variation also from other strain, like balb/c.
Are these information on the primary assembly file?
If I want to, How can I use the patch files for building the index? Just concatenate the files?
Or use the toplevel file for indexing?