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 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 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
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