[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
More information about the Genome
mailing list