Good Morning Sina: Please note, you can view the table schema for any table in the genome browser via the "tables" link in the blue navigation bar. Select group: Variation and Repeats, table: rmsk and then "describe table schema"
Note the definition of genoName, genoStart, genoEnd: genoName chr1 varchar(255) Genomic sequence name genoStart 10000 int(10) unsigned Start in genomic sequence genoEnd 10468 int(10) unsigned End in genomic sequence You can select these from the genome browser with the MySQL command: mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e "select genoName,genoStart,genoEnd from rmsk;" hg19 --Hiram Vivekanandan, Sina wrote: > Hi > > I am having trouble understanding the table for repeat masked regions from > UCSC. > What I was looking for is absolute genomic coordinates so as to use those > coordinates > to remove the repeat regions in a coordinate based file that I have. What I > find > are 6 coordinate based columns namely: genoStart, genoEnd, genoLeft, > repStart, repEnd > and repLeft. How do I use all these to find the absolute coordinates of the > repeat > regions? Please help. > > Thanks and regards > Sina K V _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
