Below follows a question and below that my reason for asking the question. Perhaps reading the "reason" part is unnecessary.
I need to find a way to convert the genomic location chromosome X, position Y in the rat genome into a corresponding position in the mouse genome (if one is known to exist). How do I do that?
The reason I am asking is that I want to find out whether some pirna clusters are conserved between different species. As the pirna reads themselves are known not to be conserved I need to use a roundabout method: I will check whether a cluster in the rat genome has a cluster in the corresponding position in the mouse genome.
As input, I have two lists - one from the rat genome, one from the mouse genome- that show pirna clusters and their locations. Since the rat and mouse genomes have many insertions and deletions I can't merely check whether the cluster found at chromosome X, position Y in the rat genome has a corresponding cluster at chromosome X, position Y in the mouse genome. Hence, I need a way to translate genomic locations between these two species.