Hi Peng, The program is sorting by genome coordinates. Ranked by first genome location (query coordinates), then second genome location (target coordinates). The options are to allow the user to sort by both or either one of the genome coordinates (if available). These three cases allow the program to be used for a variety of purposes.
I hope this information is helpful. Please feel free to contact the help mailing list again if you require further assistance. Best regards, Jen UCSC Genome Browser Support http://genome.ucsc.edu/contacts.html [email protected] [email protected] On 6/22/10 12:48 PM, Peng Yu wrote: > I tried some example and want to understand what pslSort bases on for > sorting. So far, I don't see clear what the sorting criterion is. > > The help page is sparse for me to understand. Would you please let me > know how psl files are sorted? > > What are the two stages for? Why are there two stages rather one > stage? I think that g2g option sort the alignment based on genomic > location. But is it the start (or end, middle of the alignment)? What > the option 'dirs' is based on? > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
