Hello The genoStart/End are the genomic coordinates of the match. The repStart/End are the repeat sequences coordinates of the match. These definitions are in the schema you are viewing in the column description. Comparing against the actual data can also help: click on the "alignment details" link from the details page to view the alignment along with coordinates can help buy visualizing the data.
This table is in psl format: http://genome.ucsc.edu/FAQ/FAQformat#format2 Some coordinate help: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms This information will be important to help understand the actual alignment start base and strand (again, compare to browser track in assembly viewer to confirm). Thanks, Jennifer Jackson UCSC Genome Bioinformatics Group Rapoport Alexandra wrote: > Greetings! > I have a question about 'Variation and Repeats' group of data: > > Two pairs of coordinates are given in the rmsk table - (genoStart, genoEnd) > and (repStart, repEnd). What is the difference? > For example (entries from the example supplied in 'Schema for RepeatMasker': > > 585 318 230 38 0 chr1 15264 15355 -249235266 - MIR3 SINE MIR > -119 143 49 5 > 585 239 338 148 0 chr1 18906 19048 -249231573 + L2a LINE L2 > 2942 3104 -322 7 > > at what position will the repeats actually start? > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
