I cannot get LiftOver to work from GRC38 [Human Dec. 2013 (GRCh38/hg38)] to HG19 right now, as all coordinates are leading to 'unmapped'. "Mapped" is empty. I have a simple .wig file with the following structure:
1 12345 12346 Coverage
And yet it always fails to LiftOver the file to HG19. I've tried converting the file to an interval file, a bed file, a bedgraph file, and a wig file, which have all not worked. Attempting to use LiftOver after assign the file as a "wig" file led to the following error:
The server could not complete the request. Please contact the Galaxy Team if this error persists. Uncaught exception in exposed API method:
{ "tool_id": "liftOver1", "tool_version": "1.0.4", "inputs": { "input": { "values": [ { "src": "hda", "keep": false, "hid": 1, "id": "bbd44e69cb8906b501c312b120661cd6", "name": "GRCh38.illumina.breast.wig (as interval)" } ], "batch": false }, "to_dbkey": "/galaxy/data/hg38/liftOver/hg38ToHg19.over.chain", "minMatch": "0.95", "multiple|choice": "0", "multiple|minSizeQ": "0", "multiple|minChainQ": "0", "multiple|minChainT": "0" } } .........
Any help would be most appreciated.
P.S. - note that attempting to perform an HG19 -> HG18 Liftover of the same file also did not work, so I don't believe it is an issue with the 'chain' file.