Hi, I have a few questions about human and chimp self chains. There is no chainSelf for pt2 or pt3, but I noticed that a chainSelf track is listed in the table browser on the genome browser test site. However, when I select this from the menu, I get the error "Could not find table info for table chainSelf in db panTro2." Is this a mistake or is there no self chain available for chimp?
I did find a previous post that discusses pt2 self chains: https://lists.soe.ucsc.edu/pipermail/genome/2007-December/015138.html . I downloaded the chained chimp alignments from the vsSelf directory on the test site (http://hgdownload-test.cse.ucsc.edu/goldenPath/panTro2/vsSelf/ ). Strangely, there are 50 times more chains for chimp than for hg19, and indeed, if I filter and process the pt2 chains into a bed file, they cover 32.57% of the genome. This seems quite high compared to human; running bedCoverage on the hg19 chainSelf track gives a genome- wide coverage of 19.9%. I am able to replicate the hg19 chainSelf track from the human chains, so I don't think this is a problem in the way I'm processing the chains. In addition, running the same procedure on the rheMac2 self alignment chains, which are similar in number to human, produces a self chain that covers 14% of the rheMac2 genome. In short, I have two questions: (1) Is there a pre-computed chimp self chain track? (2) If not, what's the best strategy to make one? The available panTro2 self alignments seem very different than those that are available for hg19 and rheMac2. Do you have a sense of why the panTro2 alignments have so many more chains? I want to make sure that the increased coverage of the genome by the self chain I computed is not an artifact of something about the way the chains were constructed. According to the comments in the chain files, the matrices used seem to be somewhat different, but I don't have a great sense of how this influences the results. Finally, I have one other unrelated question. In the multiz46way alignments, how consistent is the meaning of the lowercase masking? Have RepeatMasker and Tandem Repeats Finder been run on all included genomes? Thanks, Tony _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
