Is anyone familiar with how Tophat is running Bowtie? I am attempting to modify the default settings that Tophat specifies for Bowtie to improve alignments. thanks. Previous response suggested -g, -k, and -m options from within tophat. I am not getting tophat to recognize the -k option. just get the tophat: option -k not recognized are you able to get this to work? It seems like the appropriate options in bowtie would be -n, -a, --best, and --strata. But tophat does not recognize. The most critical I think would just being able to view the number of valid alignments in order (best->worst). suggestions? thanks.