Jennifer Jackson wrote:
> Hello John,
> 
> Sorry to hear about the problems transferring data over to Galaxy. It is 
> a long process. It would be much better to download the files locally 
> and use some of the utilities from the kent source tree.

I'm in the middle of trying this. These files are pretty big though.

> 
> Some popular MAF options are below.
> 
> You could also look at the maf* programs from the utility set and see 
> which will perform the exact function(s) that you need:
> http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities
> 
> Hopefully this helps!
> Jennifer

Thanks for the pointers

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