I have a question about the default liftover tool behaviour and I'm not sure if this is a feature or a bug :)
The example below is MM9 data which we need to move to HG18 (yes, we are abusing the tool by lifting between species but that's what we need to do!). The liftover tool at http://genome.ucsc.edu/cgi-bin/hgLiftOver will happily lift them back to MM8 (eg), but refuses to lift any of these regions over to HG18, complaining that they overlap and rejecting them all. I can think of situations where a BED file should not contain overlapping regions, but there are plenty of situations where it's desirable - is there a reason for the liftover tool to refuse to work on overlapping segments when moving to a different species? We know they're overlapping but we still want them lifted over and it seems happy if the liftover is within compatible MM assemblies? Thanks in advance for any suggestions you can offer. ======sample overlapping mm9 data=========== chr8 66952484 70952484 + 8-64991884 chr8 67015638 71015638 + 8-65055118 chr8 67029674 71029674 + 8-65069154 chr8 67068626 71068626 + 8-65108106 -- Ross Lazarus MBBS MPH Associate Professor, Department of Population Medicine; Director of Bioinformatics, Channing Laboratory 181 Longwood Ave., Boston MA 02115, USA. Tel: +617 525 2730 Fax: +617 525 0958 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
