Hi Onur, BED coordinates are zero-based, half-open. See: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 and http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms
The coordinate range "chr17 7520197 7520197" in BED format specifies a region of size 0. Instead, use: chr17 7520196 7520197 (This is equivalent to chr17:7520197-7520197, which is what we call "position" format . . . this is the same format you see in the Genome Browser.) When I convert the corrected BED coordinates using the web interface, I get: chr17 7579471 7579472 (which is equivalent to chr17:7579472-7579472 in position format). If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 7/6/12 10:07 AM, Onur Sumer wrote: > Hello, > > I am using the command line liftOver tool (for 64-bit linux) together > with the chain file hg18ToHg19.over.chain to convert genome coordinates > from hg18 to hg19. Command line tool fails to convert most of the single > position coordinates, in other words coordinates with the same start and > end positions cannot be converted. > > Below is an example line from the input file: > > chr17 7520197 7520197 > > And the output in the unmapped file for these coordinates is: > > #Deleted in new > chr17 7520197 7520197 > > However, when I use the web-based version > (http://genome.ucsc.edu/cgi-bin/hgLiftOver), the same data is > successfully converted from hg18 to hg19. > > Here is the input that works for the web-based version: > > chr17:7520197-7520197 > > And the conversion result is: > > chr17:7579472-7579472 > > > Do you have an idea why the command line tools does not work for such > coordinates. Are the default parameters of the web-based version > different than the command-line version? Or, can it be a bug in the > command line tool? Or, maybe I am missing some point. > > Thanks, > Onur Sumer > Computational Biology Center, > Memorial Sloan Kettering Cancer Center > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
