I am trying to find where the 20bp probes I have, lie on the mouse genome. I am trying to tune the parameters to try to match the results that I get when I search it on UCSC. I am hoping someone has some hints into tuning blat.
For reference I am using the following commands for my current results:
gfServer start -tileSize=11 -minMatch=1 -maxGap=2 localhost 3000 Index/mm10.2bit gfClient localhost 3000 ../mouse Output/test.fa Output/test.psl -t=dna -q=dna -minScore=10