Hello Tsunglin, You are correct: the liftOver tool is used to map coordinates in one assembly to coordinates in another. It uses a "liftOver chain" file, described here:
http://genomewiki.ucsc.edu/index.php/Chains_Nets http://genomewiki.ucsc.edu/index.php/Minimal_Steps_For_LiftOver BED format is described here: http://genome.ucsc.edu/FAQ/FAQformat#format1 If you have further questions after looking at these links, please feel free to email us again at [EMAIL PROTECTED] -- Brooke Rhead UCSC Genome Bioinformatics Group On 10/31/08 03:46, Tsunglin Liu wrote: > Dear UCSC genome browser scientist, > > I have a question in mapping the genomic coordinates between two close > species using liftOver tool. > > I am trying to do a whole genome alignment between two yeast strains. > I have done the following. > 1) collect the chromosomes of the two yeasts. > 2) use blastz to align the two sets of chromosomes and obtain the > alignments in lav format > 3) convert lav into axt using lavToAxt > 4) thread the aligned segments into chains using axtChain > 5) do Net procedure using chainNet > > I obtained the final alignment in net format. What I want eventually > is to map the coordinate in one genome to the other. I learned that > lifeOver tool can do this task, can it not? I ran into some troubles > using the liftOver tool. Typing "liftOver" in my terminal showed me > that it requires files in BED format. Do you know if there is a tool > to create such a file? All I have now are the chromosomes in fasta > format. Another question is that one of the argument is in chain > format, I am wondering why it does not take the alignment in net format? > > Appreciate your help! > > Sincerely yours > Tsunglin Liu > > Postdoctoral Researcher > Biodiversity Research Center, > Academia Sinica, Taiwan. > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
