Thanks, I'll re-do the conversions using the BED format. ------------------------------------------------------------------------- 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 -------------------------------------------------------------------------
On Tue, 22 Sep 2009, Brooke Rhead wrote: > 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
