Hello Eric, A description of the chain format is located here:
http://genome.ucsc.edu/goldenPath/help/chain.html Note that when the strand value is "-", position coordinates are listed in terms of the reverse-complemented sequence. Therefore, to compute the coordinates for the mouse position in your example strand, you need to subtract qStart and qEnd coordinates from qSize: The mouse end coordinate in Genome Browser format is: 155630120 - 19704 = 155610416 The mouse start coordinate in Genome Browser format is: 155630120 - 52644034 = 102986086 Note that you also need to add one to the start coordinate, as the Genome Browser uses a 1-based coordinate system for display. (See further explanation here: http://genome.ucsc.edu/FAQ/FAQtracks#tracks1 and here: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms .) So, the Genome Browser mouse coordinates become: chr4:102986087-155610416 Which is what is displayed on the chain details page. I think this explanation of chain format should answer your question #2 as well, but if not, please feel free to write back to us at genome#soe.ucsc.edu. -- Brooke Rhead UCSC Genome Bioinformatics Group On 06/03/09 18:12, [email protected] wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
