Hi Suzan,

This would be the expected gap between the paired end data when aligned to the genome. The sequencing source should be able to let you know the library target fragment size. The length of the resulting reads would be subtracted from the fragment size, leaving the "inner distances", which can then be reduced to the "mean inner distance" for the sequencing run.


This can be difficult to know with absolute certainty. You may need to map the data first and then examine the results to see if the estimate is correct or not. So, if you are able to get the information, then it would be good to know, otherwise using the default should be a fine place to start. Jeremy will likely comment if there is more advice (he authored Galaxy's TopHat wrappers).

Best,

Jen
Galaxy team

(More details if you are interested ...)

On the TopHat tool form, the parameter is defined in the "Tophat parameter list". For the version of the tool in Galaxy, there is no default, but we supply the "20" default as a starting place, since it is a required parameter.

-r 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. There is no default, and this parameter is required for paired end runs.

This can be compared with the current full description in the TopHat online manual, which is updated for Tophat2 (not yet available on Galaxy Main).
http://tophat.cbcb.umd.edu/manual.html

-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.

--mate-std-dev <int> The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp.


On 8/8/12 11:10 AM, suzan katie wrote:
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


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Jennifer Jackson
http://galaxyproject.org
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