to run tophat one has to provide a parameter: "Expected inner distance between mate pairs" with the tag "-r"
suggested by , this parameter seemed to be relied on read length: "For example, if your fragment size is 300 bp and read length is 50 bp, the inner distance is 200"
my questions are:
1) Dose this parameter mean the expected distance between two genomic loci mapped by two reads?
2) what does the "fragments size" mean and how to decide this value?
Sincerely hope that you wise guys can give me some tips.
Thanks in advance!