Hi Jia, Yes, you could probably do this from the net files, looking for large gaps in the chimpanzee chain/net. These pages should help you understand how our files are made and give you some ideas about how you'll need to manipulate them.
- http://genome.ucsc.edu/goldenPath/help/net.html (information on our download net files: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/vsPanTro3/) - https://lists.soe.ucsc.edu/pipermail/genome/2006-August/011382.html (some information on our mysql net tables: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/netPanTro3.txt.gz) - http://genomewiki.ucsc.edu/index.php/Chains_Nets - http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=primateChainNet I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 6/21/11 12:06 PM, Zeng, Jia wrote: > Hi, > > I'm fairly new to the Chain and Net tools so I apologize if this is an > obvious question. > > What I am trying to do is to compare the genomes of human and chimpanzee and > identify the mediate-sized (up to several kb) human insertion regions (ie, > the regions only in human genome that are in between two adjacent alignments > between human and chimpanzee). From what I read about the tools such as > LASTZ, Chain, Net etc, I think I should utilize the chain and net tools to > accomplish the task but I'm not certain how should I go about doing it. > > If anybody could kindly offer any input regarding this, it'll be greatly > appreciated. Thank you in advance. > > - Jia > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
