If I use Paired-end sequences for 'Tophat for illumina' or 'Tophat 2', I need to type in a 'mean inner distance'. According to the definition of this parameter,
|-r/--mate-inner-dist <int>||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 only know the average length of reads is 101bp but am not sure how long is fragments selected for sequencing (I did ask for it and waiting for the answer from the sequencing company).
And how about the standard deviation for the distribution on inner distances between mate pairs?
|--mate-std-dev <int>||The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp.|
Anyway, I tried to use the default parameters in my local Galaxy, but it seems not working. I cannot attach a error image here.