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
