tophat fr-firststrand and fr-secondstrand

Question

[biolab]

Dear all,

I have a RNA-seq data that is based on dUTP method, so I should use fr-firststrand option in tophat. For curiosity, I also tried fr-secondstrand option, I found the number of lines of SAM files are different using these two options. For most of the lines, one option gives XS +, and the other gives XS -, or vice versa. How does this happen? Your suggestions and comments are highly appreciated. THANKS