Hi, thank you you reply make me clear about the difference~~
Best Wishes. On Fri, Jun 26, 2009 at 5:51 AM, Jennifer Jackson <[email protected]> wrote: > Hello, > > Using -fine will definitely cause different results as webBlat does not use > -fine. Also, the length of your probe may cause problems (lengths shorter > than 25 bases). See "About Blat" at this link: > http://genome.ucsc.edu/cgi-bin/hgBlat > > The exact version of BLAT (and the options used) between the line command > version, the version used to align track data, webBlat are not identical. > Differences in hardware can also cause small changes. Therefore, exact > duplication of results is never expected for all cases. > > The best parameters for you to use are those that give the best answers for > your experiment given the amount of compute resource available. The > parameters used for webBlat are those that provide the best answers along > with considerations to speed and optimized utilization of UCSC's resources. > The parameters used for tracks vary considerably between the different > datasets. > > I hope this helps even though it is not an exact answer. If you have an > specific example representative of a larger group of differences (not a > single case out of many identical results) that you think cannot be > explained by this, you can send it to me directly (not the entire list) and > we can give some feedback. Include your exact line commands/web input for > each example and enough data that each result can be duplicated. > > Thanks, > Jennifer Jackson > UCSC Genome Bioinformatics Group > > > Daofeng Li wrote: > >> Hi, >> yes i noticed that....but sorry i can not understand C language >> command line i use add -fine and -q=rna used to map probe of microarray to >> genome >> so maybe that cause the inconsistent from Jim's formula? >> >> On Wed, Jun 24, 2009 at 10:13 PM, Hiram Clawson <[email protected]> >> wrote: >> >> >> >>> Please note: >>> >>> http://genome.ucsc.edu/FAQ/FAQblat >>> >>> --Hiram >>> >>> >>> >>> Daofeng Li wrote: >>> >>> >>> >>>> Hi, >>>> >>>> i think this problem might be discussed for many times and i do find som >>>> search results for that >>>> one mail i searched is of Jim which contains: >>>> //// >>>> Hmm. You could just use the -out=blast option if you >>>> really want a drop-in replacement. Otherwise try >>>> >>>> percentId = 100.0 * (match + repMatch) / >>>> (misMatch + match + repMatch + qNumInsert + tNumInsert) >>>> ///// >>>> >>>> i had try that formula,find the result output by command line blat still >>>> different with webblat... >>>> can anyone give another calc method? or something of mine wrong? >>>> >>>> Best Wishes. >>>> >>>> >>>> >>> >> >> >> > -- Daofeng Li,PhD Candidate China Agricultural University _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
