Thanks Angie and Jennifer - Angie: Not yet but will take a look. Jennifer: thanks, yes we probably need to figure out how to do this 'properly' - this project seemed so simple to start with :)
On Fri, Aug 21, 2009 at 2:34 PM, Angie Hinrichs <[email protected]> wrote: > 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 :) > -- 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
