[Genome] use of Batch Coordinate Conversion (liftOver)

[philippe.dessen@igr.fr]

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