I am new to using Tophat. I am trying to figure out the mean inner distance parameter. Tophat's documentation states "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. The default is 50bp."
I have 100 bp paired end illumina reads. What does Tophat mean by "fragments"? and what does "each end" mean?
Thanks for the help! Nikelle