Hello Jorja, I have two suggestions for you that might solve this problem. The first is to use BED formatted positions as input:
http://genome.ucsc.edu/FAQ/FAQformat#format1 The probe IDs will be retained in the 4th field, "name". The second suggestion is to also look at the "Display failure file" link (under the "View Conversions" link) to see the probes that did not lift to mm9 successfully. If you still have questions/comments for us, please feel free to contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 09/22/09 15:35, Jorja Henikoff wrote: > Hello, I am using your useful liftOver tool > (http://genome.ucsc.edu/cgi-bin/hgLiftOver) to convert the locations of > 2.1m probes on a NimbleGen array from mouse mm8 to mm9. It works fine > except for one thing. Because I have to strip the probe id off the > file before I submit the positions, I can't tell what probes were not > remapped. For instance, I have 122,701 probes on chr9 but only 122,686 > were mapped to mm9 so now I have to somehow figure out which ones > weren't. FlyBase has a similar tool which always returns the same > number of locations as input, returning "chr9:?-?" when it can't > map a location, making this task easier. > > ------------------------------------------------------------------------- > Jorja Henikoff [email protected] > Fred Hutchinson Cancer Research Center FAX: 206-667-5889 > 1100 Fairview AV N, A1-162, PO Box 19024 Seattle, WA 98109-1024 > ------------------------------------------------------------------------- > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
