What genome assembly are you using? Can you provide an example 61-mer that behaves as you said?
When blast output is chosen with blat, it breaks the alignment into exons and outputs a blast record for each. -Galt 5/23/2011 12:39 PM, Wang, Jianjun (NIH/NCI) [C]: > Hi, > > I'm using local blat to simulate searches on ucsc web site. I follow the > suggestions from UCSC Blat FAQ using this parameter set: > blat -stepSize=5 -repMatch=2253 -minScore=0 -minIdentity=0 database.2bit > query.fa output.psl > > However,sometimes I don't get hits for many 61-mer queries with 98-100% > identity to the genome. If I take those queries that have missed any hit and > repeat the same blatting, lots of hits are reported! I know this is hard to > believe but I double-checked again and again, that is what happened. I'm at > the ends of my wits. The only difference I used from the above parameter set > is that I used blast output rather than psl, which you wouldn't think matters > to the search itself. > > Could someone enlighten me? > > Thanks, > Jianjun Wang > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
