Hi Ross, Sorry if I missed this, but have you already tried liftOver -multiple?
Angie ----- "Jennifer Jackson" <[email protected]> wrote: > From: "Jennifer Jackson" <[email protected]> > To: "Ross Lazarus" <[email protected]> > Cc: "Anton Nekrutenko" <[email protected]>, "Dawn Demeo" > <[email protected]>, "Blanca Elena Himes" > <[email protected]>, [email protected], "Annerose Berndt" > <[email protected]> > Sent: Friday, August 21, 2009 11:19:41 AM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] liftover tool questions > > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
