Dear Maria, Actually the information you are looking for can be found in the .net files found on our downloads server. Here is an example url for the net file for the hg18 vs. mm8 chain (you will have to change the url according to your assemblies of interest):
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/vsMm8/hg18.mm8.net.gz These files can be processed using the net* utilities and C libraries found here: http://hgdownload.cse.ucsc.edu/downloads.html scroll down to "Source Downloads" -> "UCSC Genome Browser source download" For a brief list of all the utilities you can see our wiki page: http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities If you have further questions, please contact the mailing list again. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Xin Ma" <[email protected]> To: [email protected] Sent: Wednesday, August 25, 2010 6:15:08 PM GMT -08:00 US/Canada Pacific Subject: [Genome] How to tell the chain information from maf file Hi, I am just wondering how to tell the chain information in the maf file. eg, how to tell the start of the chain and the end of the chain and if two pieces of alignment which have gaps in between are actually in one chain. Thanks, Maria _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
