I am trying to use the command line version of liftover with the available chain files to map locations from the Drosophila melanogaster genome to the other Drosophila genomes. My problem is that I am getting different results between the web and the command line versions. For instance, lifting the following coordinates between D. melanogaster and D. ananasae (dm3 to DroAna3) gives me the following result Dmel: chr2R 12750470 12755218 aaa 1000 - Dana scaffold_13266 13843857 13848583 aaa 1 +
However, if I use the following command line using (dmel_coords.bed containing the previous bed coordinates): $ liftOver dmel_coords.bed chainFiles/dm3.droAna3.all.chain dana.lift dana.unMap dana.lift is an empty file while dana.unMap as the following line: #Split in new chr2R 12750470 12755218 aaa 1000 - Why the discrepancies? I also get similar results with other genomes while some give me the right answers (for instance with D. Simulans using the dm3.droSim1.all.chain file give me the right result). I downloaded the most recent chain files yesterday. Is there something I am not doing right? Can't figure it out... Thanks -- Marco Blanchette, Ph.D. Assistant Investigator Stowers Institute for Medical Research 1000 East 50th St. Kansas City, MO 64110 Tel: 816-926-4071 Cell: 816-726-8419 Fax: 816-926-2018 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
