Hi Vanessa,

Mean inner distance can be thought of as being the estimated gap left between the two ends of the paired reads. This is from the manual (also at the bottom of the Tophat tool form):

-r  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.

In short, take the insert size, subtract the length of both sequenced ends, and that is the "Mean inner distance".

Best,

Jen
Galaxy team

On 11/18/13 10:08 AM, Vanessa Lattimore wrote:

Hi Jen,
I was hoping you would be able to clarify something for me. What is the mean inner distance between mate pairs in the TopHat tool? I can't find a consensus online on what it is and everything I have found seems to be guesses.
My data was run on the HiSeq, and the average insert size was ~200 prior to all adaptors being removed. Do I go off this to determine the inner distance or is there a pipeline of tools I need to use to accurately determine it?
Your help would be greatly appreciated!
Many regards,

Vanessa.

-- 
Jennifer Hillman-Jackson
http://galaxyproject.org