Hi Susanne, Now that the question has been clarified and discussed here, we are now recommending that you use liftOver for SNP locations.
Apologies for misunderstanding your question at first. It was thought to be a question about mapping complete Ortholog (gene) positions, not Orthologous SNP positions. Since there are specific tracks for mapping genes (TransMap) that was the recommendation. Especially for closely related species, the results from liftOver and the Conversation track very similar. The tools exist for liftOVer that will give the mapping answer in a format that you want. To solve the starting position problem, it is suggested to utilize the "name" column of the input BED file to place informative data. Keep the data as a single string (no spaces). You are likely using a BED6 (to include strand) so the name column would be the 4th and already in your input. http://genome.ucsc.edu/FAQ/FAQformat#format1 Hopefully this helps, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Susanne Knapp" <[email protected]> wrote: > From: "Susanne Knapp" <[email protected]> > To: "[email protected]" <[email protected]> > Sent: Wednesday, January 27, 2010 8:32:52 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] ortholog positions human chimp > > Dear UCSC, > > I have discovered the LiftOver function on your website which I wanted > to use to convert a list of 12,000 positions in the human genome to > their ortholog positions in the chimpanzee genome in order to see and > plot their location. However, using the LiftOver function, I only was > able to create a list of output positions, where I can't see anymore > to which position on the human chromosome they relate, and as some > positions fail to be mapped (due to gaps in the chimp chromosome?), > it is impossible to keep track as the failed markers are listed in a > separate file. Any better way to do this? > > Looking forward to your solution to my problem, > > Kind regards, > > Susanne Knapp > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
