[Genome] use of Batch Coordinate Conversion (liftOver)

[Brooke Rhead]

Hello Philippe,

Thank you for the excellent suggestion.  We will keep it in mind the 
next time this section of our site is undergoing an upgrade. As a 
workaround, you could try using BED4 format as an input instead.  If you 
add a unique name after each line of input in the BED file (perhaps just 
number the lines, 1-1000), you will still get two files, one for 
successfully converted records and one for failed conversions, but you 
will be able to distinguish which records were successful and which failed.

I hope that the workaround will help you with your current task.  If you 
have further questions or feedback, please do not hesitate to contact us 
  again in the future.

-- 
Brooke Rhead
UCSC Genome Bioinformatics Group



philippe.dessen at igr.fr wrote:
> Dear colleagues,
> 
> 
> I have tested your utility : Batch Coordinate Conversion (liftOver)  on the URL 
> http://genome.ucsc.edu/cgi-bin/hgLiftOver
> 
> My goal is to map all probes from a 244KK CGH Agilent (defined in hg17) 
> in hg18 coordinates.
> 
> There is no problem to upload a file (either in compact format chr:x-y or in BED format
> (either on your site) or on my MacOSX.
> But I do not understand how is it possible to have a good correspondance 
> between the origin file and the target file, because there are some unmapped probes in hg18
> 
> For example : with a file with 10000 probes (coordonnates) the result is 9996 correspodance
> and 4 non mapped ..
> The result file is only 9996 lines without position of unmapped probes 
> 
> It would be better to have a result file with 2 columns :
> oldposition    newposition
> 
> for all the entries ???
> 
> Thanks for an explanation...
> 
> best regards
> 
> Philippe Dessen
> 
> 
> 
> 
> 
> 
> 
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