Hi, I have two questions.
Question 1: I have downloaded hg18_mm9.all.chain.gz from http://hgdownload.cse.ucsc.edu/goldenPath/hg18/vsMm9/hg18.mm9.all.chain.gz I just arbitrarily look at some chain to see I understand the format. When I look at header and 1st block of chain 4 in the file as shown below: chain 515669635 chr1 247249719 + 884177 58785354 chr4 155630120 - 19704 52644034 4 48 0 6 So I went to genome browser to enter the coordinates of the 1st aligned block, which is 48 bps, in human i.e. chr1:884177-884224, and I set 'mouse chain' to 'full'. When I clicked in the red colored mouse, the browser displayed the following lines on top of the report: ================================================== Mouse (July 2007/mm9) Chained Alignments (4) Human position: chr1:884178-58785354 size: 57901177 Strand: - Mouse position: chr4:102986087-155610416 size: 52624330 Chain ID: 4 Score: 515669635 Approximate Score within browser window: 1655 ... ================================================== To me, the human chain chr1:884178-58785354 is said to align to mouse chr4:102986087-155610416, but why it is different from the chain 4 header information in the download hg18_mm9.all.chain. Am I right? What might be wrong? Question 2: According to header of chain4 in the download file, mouse block begins with chr4:19704-52644034. But when I checked the mouse genome from chr4:19704-..., it contains all N's, how can N's be included in the alignment? Thanks, -- Eric _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
