Higher tileSize increases memory, increases speed, decreases sensitivity slightly.
The default tileSize 11 is very good. On rare occasions you see 10 or 12 used. Smaller tileSizes tend to lead to dramatically longer runtime. It's a little complex to state easily in a formula because there are multiple phases internally that have each different characteristics. The default stepSize is just tileSize. This means that you are sampling a position of the genome every stepSize bases. For PCR primer searching, we leave tileSize at 11 and lower stepSize to 5 for increased sensitivity. Of course this will also cause the runtime to grow. Increasing sensitivity means increasing the number of hits, and each hit that has to be explored can take a lot of processing. And of course, whatever generalizations one would make, the real power, speed, and memory-required will depend on the characteristics of the genome, the queries. Not to mention several command-line switches that are available. But luckily the defaults have good performance and sensitivity for a wide-range of applications. If you are doing short-reads then perhaps one of the many good freely available short-read aligners like would be useful. BLAT is free for non-commercial use. -Galt Ar 3/8/2010 7:03 AM, scríobh Fungazid: > Hello people, > > > About gfServer/gfClient : > > I see that higher -tileSize leads to higher memory requirement. Does higher > -tileSize expected to decrease detection power ? > In addition, should higher -tileSize enhance the speed of gfServer/gfClient ? > > And, what is the -stepSize and how it effects the detection power, speed and > memory requirement ? > > > Thanks, > Avi > > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
