I'm looking for a 'protocol' or I would like to know the best way to create a chain file in order to get the new coordinates of a new assembly of a given genome. I have an old genome, with a gtf file, and a new genome (only the fasta). I would like to create a new GTF, and I'm thinking about Crossmap, but first, I need this chain file... I have read something about blat if the specie is the same (my case)..: http://genomewiki.ucsc.edu/index.php/Minimal_Steps_For_LiftOver, but my genome is larger than 4Mb!
Anyone knows a pipeline o protocol for doing this?
Thanks in advance,