[galaxy-user] Can I convert paired-end datasets into single end ones?

Dear All, I have some paired-end datasets to be analyzed, but I am not sure about their Mean Inner Distance between Mate Pairs. Can I convert these paired-end datasets into single-end ones and use them as single-end dataset as follows? 1) Use the tool "Manipulate FASTQ" to convert the sequence of reverse reads into its reverse-complement counter part, so that all of the reverse reads actually become forward reads. 2) run Tophat on the manipulated datasets as single-end ones. Thanks. Jianguang