I'm looking to do alignment to multiple mouse strains (genetic contributions from different strains DBA/2, C57BL/6, C3H). The current plan is to merge the various genomes (and gtf files) to figure out contribution from each of the strains.
So the question is, are there different gtf files for the difference strains? I've managed to locate the genomes themselves, but have not managed to locate the gtf files.
Second question is, is there a better way of doing this?