[Genome] canFam2ToHg18 liftOver

[Smith, Brandon]

Brooke:

I'm interested to know what tool you would suggest to use for small
regions.  I have used liftover with good success for 8bp regions, but if
there's something better I'd love to know.

Thanks,


Brandon Smith 
  
 
-----Original Message-----
From: genome-bounces at soe.ucsc.edu [mailto:genome-bounces at soe.ucsc.edu]
On Behalf Of Brooke Rhead
Sent: June 13, 2007 2:49 PM
To: Emmanuel Buschiazzo
Cc: genome at soe.ucsc.edu
Subject: Re: [Genome] canFam2ToHg18 liftOver

Hello Emmanuel,

If you would like to send us the file you are using for input (no need 
to copy the entire list -- attachments get stripped from it, anyway), we

can take a look at what is happening.  Or if you would rather, just send

us a sample of your file that will illustrate the strange behavior.

Also, can you describe what kind of regions these are?  (E.g., are they 
entire gene regions, just small regions of genes, not genes at all, 
etc.?)  Perhaps we can suggest a different tool that would be more 
useful than liftOver in this case.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Emmanuel Buschiazzo wrote:
> Hello team,
> 
> I have use the canFam2ToHg18.over.chain.gz file with the stand-alone 
> liftOver.
> 
> Two unexpected things happened:
> -all entries in the output appeared twice (therefore I then used
jkUnik)
> - from 83013 sequences from the dog genome, only 52371 corresponding 
> human sequences were found and only 2867 were unmapped (To my defense,
I 
> can add that I had -minMatch=0.01 and I chose the multiple option;
also 
> I have successfully used liftOver with other species).
> 
> Because this strange result is specific to this file, there might be 
> something wrong with it.
> 
> Moreover, the online liftOver could not seem to handle my file, and
has 
> never game me a result page... although I might have not been patient 
> enough?
> 
> Thank you for any help with this!
> 
> Emmanuel.
> 
> <mailto:ebr26 at student.canterbury.ac.nz>
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
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