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. >>> >>> > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
