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