[Genome] Using liftover

[Heather Trumbower]

Joe:

I think you need one more argument (the file name for unmapped 
elements).    You've got "xxx" for the filename for the successful
mappings, but command-line liftOver also requires "yyy" where
a lift isn't possible.

Heather Trumbower
UCSC Genome Bioinformatics Group


On Sun, 1 Apr 2007, Joe Trubisz wrote:

> Hi...
>
> Maybe I'm a total idiot, but for the life of me, I cannot get
> liftover to work at all.
> I tried it both on linux and mac and I keep getting the same results.
> Perhaps you can explain to me where I'm going wrong.
>
> I'm trying to do a hg18-17 coordinate mapping of a human genome .gff
> file (it's in gff3 if that makes any difference).
>
> A sample of the file (ref.txt) is as follows:
>
> ##gff-version 3
> chr14	UCSC_1	mRNA	91108540	91111136	.	-
> ID=NM_001080113;Name=NM_001080113;Alias=PP8961;Note=hypothetical
> protein LOC650662
> chr14	UCSC_1	three_prime_UTR	91108540	91110276	.	-	Parent=NM_001080113
>
> I downloaded the hg18Tohg17.over.chain file.
>
> I tried liftover with -gff appearing in all places as follows:
>
> liftover ref.txt hg18ToHg17.over.chain xxx -gff
>
> and all I keep getting back is the usage page. I tried to include the
> -errorHelp, but it was of no help.
>
> Suggestions are welcome...I'm stumped!!!!
>
> Thanks,
> Joe Trubisz
> Cold Spring Harbor Labs.
>
>
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