I'm having some difficulty building the source utilities on my Mac. The online resource at UCSC is for building and installing on Linux/Unix systems. Specifically, I am using version 10.6.5. I know this is Unix-based, but is there a way to build the source on a Mac?
Thanks! -Kraig On Tue, Nov 16, 2010 at 7:54 PM, Mary Goldman <[email protected]> wrote: > 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 >> >> >> > > > -- 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
