I don't know if it is relevant to your problem, but your data does not appear to be in standard BED format.
http://genome.ucsc.edu/FAQ/FAQformat#format1 Looks like you could move the 4th column (strand) to the 6th. Move the 5th col (name) to 4th col. Put dummy score 0 in 5th col. Then you would have a bed 6. Unless you are using the commandline tool with -bedPlus=3 ? -Galt On Fri, 21 Aug 2009, Ross Lazarus wrote: > 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 > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
