Galaxy Tophat

Question

[KS]

Hello,

I am trying to run TopHat for paired end and this is my first time using Galaxy and TopHat and I have a doubt regarding what to mention in Mean Inner Distance between Mate Pairs:The default value is 20.

Should I leave the value or should I be changing the value.

What is Mean Inner Distance between Mate Pairs?

Thanks

[Vivek]

Should be the Insert size right?

Answer 1

[seidel]

From the tophat manual: 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.

You should change it to whatever you think your fragment size is, minus the length of each read. If you don't know or can't find out the insert size, make up something reasonable. It will likely be a number between 50 and 800. In fact you might benefit from taking a sample of your reads and trying both values to see if/when it makes a difference.