[Genome] Liftover dies when using BED files with 12 fields?

John Major major at cbio.mskcc.org
Wed Aug 15 08:47:35 PDT 2007


Hello UCSC folks-

I am trying to convert a large # of BED files from DM2 to DM3.
These files are all BED files using all of the 12 allowed fields ( 
http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED ).

And example line from my BED file is:
(space separated)
chr4 646375 646462 miR-1000 0 + 646375 646462 255,0,0 2 42,41 0,46
chrX 12896008 12896104 miR-1026 0 + 12896008 12896104 255,0,0 2 47,44 0,52

When I try to run liftover on these files, I get the following error:

--Reading liftover chains
--Mapping coordinates
--invalid unsigned number: "255,0,0"

According to the documentation for liftover, I should be able to use 
valid BED files.  These BED files are displayed properly via the Genome 
Browser, so am i missing something obvious here?  Do I need to enclose 
the last 4 fields in some kind of quotes?  Or does liftover not actually 
work with the last 4 BED file fields?

thanks!
john major


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