Howdy, I am getting the following error with tophat: Error in tophat: [2012-12-27 15:08:40] Beginning TopHat run (v2.0.5) ----------------------------------------------- [2012-12-27 15:08:40] Checking for Bowtie Traceback (most recent call last): File "/usr/bin/tophat", line 4035, in <module> sys.exit(main()) File "/usr/bin/tophat", line 3836, in main check_bowtie(params) File "/usr/bin/tophat", line 1473, in check_bowtie bowtie_version = get_bowtie_version(params.bowtie2) File "/usr/bin/tophat", line 1351, in get_bowtie_version bowtie_version = [int(x) for x in ver_numbers[:3]] + [int(ver_numbers[3][4:])] IndexError: list index out of range I tried Tophat and Tophat2 a couple times and always giving me the same error. The reads I am trying to map are from small RNA sequencing project. I am trying to map the unannotated reads back to the genome. I am not sure what is causing this problem, any help will be appreciated. Thank you. Luciano