Does anyone have advice on what to use for the tophat -r parameter (mate inner distance)?
For example, if the lab cuts a ~200 fragment out of a gel, that includes 92 bases of adaptor, then I subtract two reads of 36, I come up with 36 for the mate inner distance.
What did you use when you ran tophat, and what fragment size did your lab cut out of the gel?
Alternatively, has anyone tried running tophat with different values for this parameter and compared the results? (I might try this). I see that there's a default 20 bp std deviation for mate inner distance.
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