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
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