Dear all,
I use liftover browser to map the human genome coordinates to the rhesus monkey genome to find orthologs.
A region of human chromosome (a hundred to thousand bp) can be often mapped to multiple regions in the rhesus genome. The mapped regions are labeled with 1, 2, 3, etc. What is the criterion to order the outputs?
Particularly, suppose a chain in human has a counterpart chain in rhesus. From the human chain, a region hits multiple regions in rhesus genome. One of the multiple hit is in the corresponding rhesus chain. Is this in-chain hit always listed as the first, even though other hits are more similar to query region from human?
To find ortholog for a chromosome region in human, I liftover this query region to rhesus genome, and then liftover the first hit in rhesus back to human. If this liftover-back is overlapped with the query region, I consider finding a pair of orthologs.
Is this a right way to find orthologs using liftover?
Sorry for the long and multiple questions in one post.
Thanks
