Hi, The advice is to create a small shell (or other, perl, etc) wrapper script to pull off one line of the BED file at a time and run liftOver for each seperately. The "foreach" command is one option. The output file (unmapped) would need to be incrementally named for each cycle or it will clobber or not write, depending in the user's shell environment.
Hope that this helps. I'll make sure the developers know about this. There is probably a reason for the program being this way, but the can decide if/when anything needs to change. You already know that we recommend not to use liftOver for cross-species (use Conservation track instead), so I won't go into more detail about that now ;) Thanks, Jennier ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Ross Lazarus" <[email protected]> wrote: > From: "Ross Lazarus" <[email protected]> > To: [email protected] > Cc: "Anton Nekrutenko" <[email protected]>, "Dawn Demeo" > <[email protected]>, "Blanca Elena Himes" > <[email protected]>, "Annerose Berndt" <[email protected]> > Sent: Friday, August 21, 2009 7:31:47 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] liftover tool questions > > 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
