I am trying to convert wig (or bigwig) and bed (or bigbed) files from the UCSC ce11 (WBcel235) coordinates to the ce10 (WS220) coordinates. The input files were actually created using the WS241 assembly, which is not available on UCSC yet, but the chromosome coordinates are the same in WS241 and WBcel235. I have tried to do this conversion using the gui interface at usegalaxy.org and the UCSC gui but I get the no dataset available error. Are the input files not being recognized because they were made with the WS241 assembly?
Yes, there is probably a chromosome naming difference between the two genome versions. This will need to be resolved before liftOver is used. https://galaxyproject.org/support/chrom-identifiers/
The error you describe "no dataset available" might be true in Galaxy if the database 'ce11' is assigned to the inputs. There are no liftover files yet available for ce11 (including ce11Toce10) at https://usegalaxy.org. I do see the "from ce11" > "to ce10" liftover option available through the UCSC web: http://genome.ucsc.edu/cgi-bin/hgLiftOver - so use that once you have the identifiers swapped out.
Hope that helps, Jen, Galaxy team
The chromosome naming is the same. Do you have any other suggestions? Also, when I try to convert a bed from the ce10 assembly to the ce11, it does not offer ce11 as a "convert to" option (I can only convert to other species or ce6) so before I spend a lot of time trying to find the problem in the files I'd like to make sure that I will be able to convert from ce11 to ce10.
Also, if I use bed files instead of bigbed, liftOver is able to recognize the files but has no available "convert to" assemblies.