Hello, Sushmita. If you are using the command line liftOver tool to convert mm9 genomic coordinates to mm10 genomic coordinates, then yes, you will use that file to perform the conversion. The basic usage of the liftOver tool is as follows:
liftOver oldfile map.chain newfile unmapped oldfile: The file that contains your list of mm9 coordinates map.chain: The mm9ToMm10.over.chain file that you downloaded newfile: A target file that will contain the equivalent mm10 coordinates unMapped: A target file that contains any coordinates that could not be lifted over Please note that there is also a web-based liftOver tool that performs the same function and does not require you to download additional files. The web-based liftOver tool is located at http://genome.ucsc.edu/cgi-bin/hgLiftOver. Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of sushmita Sent: Wednesday, June 20, 2012 5:26 AM To: [email protected] Subject: [Genome] Query related to liftOver tool Dear Sir/Madam, I downloaded "mm9ToMm10.over.chain" file from UCSC site. But the file content is not clear to me. Can you please help me to understand that? Shall I use this file to run "liftOver" tool? Thanks and Regards, Sushmita _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
