I was able to find the "missing" alignment using blat mm9.2bit -stepSize=5 -minScore=0 -minIdentity=0 testset.txt out.ps
It also worked with or without -fine. FYI I used BLAT v. 34x2 -Galt On Mon, 24 Nov 2008, Mehta, Perdeep wrote: > Hi, > > I am using standalone BLAT to search genomic locations for several > sequences. In the test set I have 13 sequences with varying lengths > totaling 1469 bases. For some reason, BLAT produces results for all > except the last sequence. I checked that sequence by loading into UCSC > Genome Browser BLAT server and it worked fine and pretty fast. See the > attached snapshot of those results. I have tried to play a little with > the BLAT parameters, it has no effect and if I lower too much the > stepSize and tileSize it takes longer to finish. Any suggestion! > > Thanks in advance. > perdeep > > Perdeep K. Mehta, PhD > Research Informatics, Information Sciences Division > St. Jude Children's Research Hospital > 262 Danny Thomas Place > Memphis, TN 38105-2794 > Tel: 901-495 3774 > http://www.hatwellcenter.org/ > > > > > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
