General question about TopHat

[mhayes]

I am using TopHat for some analyses. The program requires the expected mean of the inner distances of the paired reads as a parameter.

However, why does the program need the expected mean inner distance? How does it use this information?

I could not find this information in the online manual.

Thanks.

[kopi-o]

I think it uses it for flagging reads as "properly paired" in the output BAM/SAM file. There may be other ways it uses it but I don't know about those.