thanks! That clarifies the issue. - atif
On 3/25/2009 8:12 AM, Jennifer Jackson wrote: > 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
