It would be helpful if you provided an example. http://hgwdev.cse.ucsc.edu/FAQ/FAQblat.html#blat5
Try setting minScore=0. -Galt On 05/18/11 10:19, Tyler Garvin wrote: > Hi all, > > I recently downloaded blat and and have been using it from my computer > (rather than using web based blat). I have been trying to use blat to gather > my own SVA data using the SVA consensus sequence from RepBase. The output > from blat, though, has never give me more than 32 results per chromosome. I > even used a number of small random sequences for my query and I still got a > max of 32 results per chromosome. > > I tried installing blat from a number of different places in the hope that I > simply had a corrupted blat executable but every download gives me the exact > same results. I have also played with a number of parameters and none of > them seem to change my results much. My database is a text file that has > paths to .nib files for each chromosome of the human genome. > > If anyone knows why this may be happening or how I should fix it I would > really appreciate it. > > Thanks > T > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
