Hello Qihui, Thank you for your questions. The ponAbe2 chains were built in the same manner as the others and all follow our zero-based start and one-based end convention. For more information on this please see our FAQ:
http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1 And this wiki on coordinate transforms: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms Best regards, Pauline Fujita, UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 09/14/11 09:14, Qihui Zhu wrote: > Dear Sir/Madam, > > I have 2 questions for liftOver tool from UCSC Genome browser. I > liftover from hg19 to 4 primate genomes: panTro3, ponAbe2, rheMac2 and > calJac3. My input is 0-based start BED file. My questions are, > > 1) For panTro3, rheMac2 and calJac3, the output varies among different > chromosomes. For instance, hg19 (chr1 14906 14907 A) can be > successfully converted to panTro3 (chr15 99530063 99530064 A ), while > hg19 (chr12 78301058 78301059 A) was converted to panTro3 (chr12 > 77844433 77844434 A ) and the corrected one should be panTro3 (chr12 > 77844434 77844435 A ) > > 2) For ponAbe2, it seems the 0-based BED input will output -1 based BED > file, so I use 1-based start BED file for ponAbe2. Is there any > different between hg19-ponAbe2 chain file and other chain files? > > Thanks in advance for your great help! > > Qihui > ---------------------------- > Qihui Zhu, Ph.D. > Molecular Genetic Research Unit > Brigham&Women's Hospital | Harvard Medical School > 221 Longwood Avenue, EBRC-404 > Boston, MA 02115 > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
