Convert Rat to Human region cordinates

Question

[aleix.arnau1990]

Dear all,

I have regions from a human genome and I want to get the equivalent regions in rat genome. I saw a paper which use galaxy to do it but the lift-over convert genome coordinates tool doesn't work (I don't know why). My data looks like this:

#chr     #start_position   #end_position
1          12123                   2342354
13        35235                  2352352
X           235235               4565757

Could someone tell me how can I convert these regions from human genome to rat genome?

Thanks!

Answer 1

[PoGibas]

Try to reformat your data into bed format (something like this):

chr1    12123    2342354
chr13    35235    2352352
chrX    235235    4565757

and convert them using online liftOver.