Hello Kadir, It appears that you are looking at the chain table rather than the net table. The mouse chain track on human shows many alignments of mouse to human, while the net track shows the best mouse/human chain for every part of the human genome. An informal (but helpful!) discussion on nets and chains is here: http://genomewiki.ucsc.edu/index.php/Chains_Nets
There are several ways you could go about doing your analysis: One of our engineers pointed out that the database tables for chains and nets are optimized for browsing, not analysis. You could instead download the mouse over.chain file for hg18 (http://hgdownload.cse.ucsc.edu/goldenPath/hg18/liftOver/hg18ToMm9.over.chain.gz) and use the liftOver utility (http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads) to map regions on human to mouse coordinates. Note, however, that cross-species mappings using liftOver can be messy, and we don't expect gene structures to necessarily map cleanly with this tool. If you are looking to map transcripts/gene structures, the TransMap track will be more useful. See this previously-answered question for more on TransMap: https://lists.soe.ucsc.edu/pipermail/genome/2008-July/016784.html If you would rather just do your own filtering of the nets and chains, for example to keep only the longest or highest-scoring ones, you can download all files in http://hgdownload.cse.ucsc.edu/goldenPath/hg18/vsMm9/ instead, and use the "netFilter" utility in our source tree. Also, you might find the AXT format easier to work with than chain & net. Links to descriptions of the Chain format, the Net format, and the Axt format can be found on this page: http://genome.ucsc.edu/FAQ/FAQformat.html I hope one of these methods and/or data formats will suit your needs. If you have further questions for us, please feel free to contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 12/06/10 10:19, Kadir Caner Akdemir wrote: > Dear Vanessa, > > I have a question regarding the Mouse Chain/Net track on genome browser. I > want to get a dataset so I can map the homolog regions in human and mouse > genomes. > > I did get the net track from table browser, however its content confused me > little bit... > > I copied beginning of the file to clarify which part I got lost: > > 585 27365 chr1 247249719 42251 43210 chr2 181748087 - 69864848 69865818 > 298960 585 12959 chr1 247249719 42258 43239 chr2 181748087 - 92905582 > 92906590 1192282 585 11032 chr1 247249719 42259 43214 chr19 61342430 - > 49168237 49169227 1501733 > > > So as you can see, nearly same segment on human genome - chr1 ~42250 - > mapped on both chr2 and chr19 on mouse genome and Im confused which one I > should use in my analysis. > > Sincerely, > Kadir Akdemir > ______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
