Hello,
Thanks for a very useful tool, blat. We are trying to use blat to design probes for microarray. We would like to see whether our probe is unique in the genome or have more than one match with at least 90% identity. The probes are 60mers and the genome is not an ordinary genome, but rather a mouse genome that was converted by bisulfate treatment - where every C was converted to T. In the manual, it says that the default for blat search is 90% identity for DNA sequences, but when trying to run a search, we also got matches that are 34 or 38 long. Is there a way to ask blat to report only on matches that are at least 90% identical out of all the 60mer (then, the smallest match could be 54 mer )? should we change the minScore ? Another question is ,if we have the (converted) chromosomes in fasta format, should we convert it to 2bit format (for faster execution) and how ? Thanks a lot, Shlomit Amar-Farkash The Hebrew University, Jeruslaem, Israel _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
