Hello, Please see our documentation http://genome.ucsc.edu/goldenPath/help/chain.html http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms
The coordinates for this chr20 chain are in the (-) strand. Chain file formats are different from many of our other file formats in that they are based on the reverse-complement strand (not converted to be positive strand). However, they are still ordered smallest -> largest in value. And the smallest coordinate is still zero-based. These chain coordinates are converted to be positive stranded and to be a 1-based start when displayed in the browser chain description page. The chromosome 20 length is: 62,435,964 Doing the math to compare the browser data points to the chain file data points: start: 62435964 - 19465389 = 42970575 end: 62435964 - 19472380 = 42963584 +1 (to convert the zero-based "smallest" coordinate) = 42963585 I hope I have addressed all of your questions, but let me know if I missed anything, Jennifer Jackson UCSC Genome Bioinformatics Group Atif Shahab wrote: > > Sorry copied the wrong row. Following is the row I find in > chr11.chainSelf > > 725, 212246, 'chr11', 134452384, 18466024, 18469085, 'chr20', > 62435964, '-', 19465389, 19472380, 80309, 77.2 > > while what I see in UCSC browser is > > *Human position:* chr11:18466025-18469085 size: 3061 > *Strand:* - > *Human position: * chr20:42963585-42970575 > <http://ucsc.gis.a-star.edu.sg/cgi-bin/hgTracks?db=hg18&position=chr20%3A42963585-42970575> > > size: 6991 > *Chain ID:* 80309 > *Score:* 212246 *Approximate Score within browser window:* 1240 > > The browser reports reports the position to be in > chr20:42963585-42970575 while what I get from the chr11.chainSelf is > chr20:19465389-19472380. > > - atif > > On 3/24/2009 2:44 AM, Jennifer Jackson wrote: >> Hello, >> >> The data reported for the region chr11:56259903-56260492 on the track >> description page represents a subset of the data from the entire >> chain record (chr11_chainSelf.id = 1118118). That is why the score is >> approximate. The track description page explains the display >> conventions in the Description section. >> >> We hope this helps to explain the data, >> Jennifer Jackson >> UCSC Genome Bioinformatics Group >> >> >> >> >> >> Atif Shahab wrote: >>> Hi, >>> >>> In the UCSC browser I get the following info >>> >>> *Human position:* chr11:56259903-56260492 size: 590 >>> *Strand:* - >>> *Human position: * chr20:56904056-56908860 >>> <http://ucsc.gis.a-star.edu.sg/cgi-bin/hgTracks?db=hg18&position=chr20%3A56904056-56908860> >>> >>> size: 4805 >>> *Chain ID:* 1118118 >>> *Score:* 38233 *Approximate Score within browser window:* 2221 >>> >>> But when I look into the mysql table for chr11. I find the following >>> >>> 725, 212246, 'chr11', 134452384, 18466024, 18469085, 'chr20', >>> 62435964, '-', 19465389, 19472380, 80309, 77.2 >>> >>> Notice that the chr20 start/end are different from what is show in >>> the browser. Does the browser use some formula to compute the >>> start/end? >>> >>> Also the chain track displays boxes joined by single/double lines. >>> Which table contains the info regarding the start/end positions of >>> these boxes? >>> >>> - atif >>> _______________________________________________ >>> Genome maillist - [email protected] >>> http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
