Hi Chuangye, A review of past parameters used for Blastz & Lastz can be found in the makedocs. These are histories of what has been done to generate data tracks for each assembly. Location is the kent source tree, but also online at: http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/makeDb/doc/
For example, in hg19.txt, searching with "lastz", has several references for chains/nets. Some of these sections point to other programs in the kent source tree (that have the run parameters), others have the parameters recorded. Kent source: http://hgdownload.cse.ucsc.edu/downloads.html -> scroll to the second section titled "Source Downloads" Comparing these parameters with the track/dataset they produced in the native track set will likely help you to narrow down the desired usage statement and also help with post-processing/filter steps. I hope this information is helpful. Please feel free to contact the help mailing list again if you require further assistance. Best regards, Jen UCSC Genome Browser Support On 7/19/10 7:56 AM, Chuangye wrote: > Dear Sir, > > I want to use blastz to produce segmental duplication fragments of gorilla > genome. Could some give me some suggestion on how to set the parameters? Or > could you give me the examples to use it to produce segmental duplications ? > > Thank you in advance. > > > Chuangye > > 2010-07-19 > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
