Hi Fabrice, You will have to obtain copies of BLAT and pslReps: http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads, both part of the kent source.
Some info on BLAT: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BLATAlign Also, once you have the command line utilities installed you can type the name of the util (blat, pslReps) to get help/documentation on that tool. If you have any additional questions, please reply to: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 2/13/12 1:28 AM, Fabrice Tourre wrote: > Dear list, > > I want to remap HG U133 plus 2 array probe sequence to genome. So I > can check which probe mapped to multiple genome position. In ucsc web > site, it is describe as: > > shows the location of the consensus and exemplar sequences used for > the selection of probes on the Affymetrix HG-U133 Plus 2.0 chip. > Consensus and exemplar sequences were downloaded from the Affymetrix > Product Support and mapped to the genome using blat followed by > pslReps with the parameters: -minCover=0.3 -minAli=0.95 > -nearTop=0.005 > > Could you share me the detail commands? I do not know how to use blat > and pslReps. > > Thank you in advance. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
