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
