How to tell which library type to use in bowtie, tophat (fr-unstrand, -firststrand -secondstrand)?

How to tell which library type to use (fr-unstrand, -firststrand or secondstrand)?

 

http://onetipperday.sterding.com/2012/07/how-to-tell-which-library-type-to-use.html

tophat install error : except getopt.error, msg: SyntaxError: invalid syntax

http://seqanswers.com/forums/showthread.php?t=17514

Error :
File "./tophat", line 1003
    except getopt.error, msg:
                       ^
SyntaxError: invalid syntax

To solve :
edit tophat

#!/usr/bin/env python2

instead of

#!/usr/bin/env python


This error comes from the difference between python2 and python3.

check your path  and version of python