Hi Kraig, You can get chainSwap utility as a part of our source downloads. You can find instructions about downloading and installing kent source utilities here:
http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads http://genome.ucsc.edu/admin/jk-install.html With the actual source download residing here: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 11/16/10 2:29 PM, Kraig Stevenson wrote: > To whom it may concern: > > My name is Kraig Stevenson, and I am a PhD student in bioinformatics at the > University of Michigan. I would like to request the chainSwap utility. > > Thank you very much! > > -Kraig > > ---------- Forwarded message ---------- > From: Jim Kent<[email protected]> > Date: Tue, Nov 16, 2010 at 3:30 PM > Subject: Re: Reverse chain files for LiftOver tool > To: Kraig Stevenson<[email protected]> > > > In general you will want to generate a separate chain file for the reverse. > I _think_ you'll end up with just a 5% less good result if you basically > swap the target and query sequences in the chain. We have a chainSwap > utility at UCSC that will do that. If this is the route you decide to take, > please contact [email protected] to get the utility. It'd be best if you > got in contact with whoever generated the chain file in the first place > though. > > Take care, > Jim > > On Nov 16, 2010, at 11:28 AM, Kraig Stevenson wrote: > > Hello Dr. Kent, > > My name is Kraig Stevenson, and I am a bioinformatics PhD student at the > University of Michigan. I have extensively used your LiftOver tool to go > between species, and I currently have a chain file that lifts coordinates > from one (non-sequenced) species to a (sequenced) species (this was given to > us by a collaborator). Now I would actually like to go in the opposite > direction, but I am not sure how to go about this. Is there a way to reverse > the chain file so that the LiftOver tool could accomplish this task? Could > the LiftUp tool be used in this situation? > > Any advice you might have would be greatly appreciated. > > Best regards, > > -Kraig > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
