Meaning of -r in Tophat 2

Question

[Arash]

Hi,

Whats meaning of -r in Tophat 2 ? For Tophat running , how can i set up it? My question is whats the meaning of 50 or 200 or 100 in this option?

Thanks

Answer 1

[Dan D]

The documentation is helpful, if you haven't yet looked at it. I'll try to add some more to their explanation of the 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.

You could also call this the "insert size." If you have access to the Bioanalyzer traces, or some other indicator of average fragment size from the library preparation process, then this is the value you would use. Take that value and subtract the total number of cycles.

[Arash]

Hi,Thanks! My fragment reads is around 140 pb for each reads.now, how much the r value? TNX again

[Dan D]

I have clearly explained the documentation which in turn clearly explains how to use the parameter. I can't answer your question with the information you have provided me.