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 -- Kraig Stevenson PhD candidate U of M Bioinformatics Graduate Program Wittkopp laboratory 1061 Natural Science Building Ann Arbor, Michigan 48109-1048 [email protected] -- Kraig Stevenson PhD candidate U of M Bioinformatics Graduate Program Wittkopp laboratory 1061 Natural Science Building Ann Arbor, Michigan 48109-1048 [email protected] _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
