My apologies Peng, please disregard this answer. It is incorrect. Please see Hiram's correct answer, if you have not already:
https://lists.soe.ucsc.edu/pipermail/genome/2010-June/022692.html On 6/22/10 1:24 PM, Jennifer Jackson wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
