Hi all,
When mapping pair end RNA-seq reads using tophat, we need to type in "Mean Inner Distance between Mate Pairs".  In galaxy, we can read the following information:
This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments
 selected at 300bp, where each end is 50bp, you should set -r to be 200. There is no default, and this parameter
 is required for paired end runs.
I think the size of fragment (here 300bp) includes not only the length of pair end reads, but also the length of adaptors. so, maybe the Mean Inner Distance between Mate Pairs should be : fragment length - pair end read length - adaptor length. Am I right? or did I miss something?  
Is it a must to type in the accurate value?
Looking forward to your reply