[Genome] (no subject)

[Brooke Rhead]

Hello Jia Hui,

The difference is that the stand-alone liftOver program has a default of 
-minMatch=0.95.  The web-based liftOver program generally has a default 
minMatch of 0.95 for same-species liftOvers and 0.1 for 
different-species liftOvers.

I tried your example lift with a setting of -minMatch=0.1 in addition to 
the -multiple option, and I was able to reproduce the web-based result:

liftOver -multiple -minMatch=0.1 oldFile hg18ToMm8.over.chain newFile 
unMapped

cat newFile
chrX    164652840       164688071       -       1
chrX    164684015       164685253       -       2
chrX    161953905       161958507       -       3
chrX    161957814       161958204       -       4
chrX    161958006       161958277       -       5

Please let us know if you have any further questions.

--
Brooke Rhead
UCSC Genome Bioinformatics Group.


JIA Hui wrote:
> Dear Sir,
> 
> I met a problem when I use liftover now. The result I got from
> stand-alone program and web based program are different.
> 
> The parameter for both program I set as default except set -multiple as
> "on".
> 
>  
> 
> For example:
> 
> I mapped "chrX   11018195          11060029          -" from Human Hg18
> to Mouse Mm8. 
> 
> Results are attached. It has five maps with web based program but no map
> with stand-alone program.
> 
>  
> 
> The figure hgt_genome_8b3_10dd90.gif is the snapshot of this gene in
> UCSC browser.
> 
> Could you please tell me what cause this difference?
> 
> Many thanks
> 
>  
> 
> Best Regards,
> 
> Jia Hui
> 
> Information & Mathematical Sciences
> 
> Genome Institute of Singapore
> 
> 60 Biopolis Street, #02-01, Singapore 138672
> 
> DID:  6478 8652     
> 
>  
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