From about 1 million segments from hg19 of the form:
chr2 111032430 111052520
I tried to re-map these to hg18 using LiftOver. LiftOver performs very well and was able to correctly map all but about 1,500 reads to the old hg18 release. In the interest of being thorough, I wanted to find an automated way to map the remaining releases back to hg18 if at all possible. So, for instance, the above (according to BLAT) would re-map to
2 111169575 111170890 2 110191298 110210043
And so on for each. Right now my data is in Galaxy. Is there a simple tool to re-map any un-mapped segments from hg19 to hg18 where LiftOver fails?