Hi, I have a question about the command line liftover utility. I'm using liftover to convert the coordinates of several million sequences from D. melanogaster (2006 release) to D. sechellia. I noticed something strange in the process. When I liftover from melanogaster to sechellia, about 12% of these sequences don't liftover. That's not a big deal to me though, because I can imagine that some of these are in unmapped regions of D. sechellia. The REALLY weird thing is that when I take the lifted (mel to sec) coordinates and lift them back into D. melanogaster coordinates, 2% of these don't lift back. Why is it that some coordinates that can be mapped from mel to sec, can't be mapped backwards from sec to mel? How does liftover work?
If it helps, I'm using a Mac for these operations. Thank you for any help with this, Joel Joel McManus Postdoctoral Fellow Graveley Lab University of Connecticut Health Center Department of Genetics and Developmental Biology 263 Farmington Ave ARB Rm E3053 Farmington, CT 06030 phone: 860 679 2092 [EMAIL PROTECTED] _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
