Tophat Inner Mean Distance

priyam21292 · 04-25-2016, 06:42 PM

Hello all,

I'm currently working on RNA-seq analysis using Galaxy. The dataset which I'm using is a paired-end data from BodyMap Project.

For the BodyMap Project, inner mean distance of 110 is recommended for TopHat. I'm trying to put different values and see the results, but the results aren't as expected.

If I'm right, I should be getting the best alignment with the recommended inner mean distance.

In this case, I've tried 50, 110, 300 and 400. But there is not much difference in the alignment summary with the given set of input. Why is that?

Michael.Ante · 04-26-2016, 12:29 AM

Hi Priyam21292,

TopHat estimates the mean inner distance itself. It uses - if given - the input value as a starting point for the optimisation. In case you provide this parameter, the computing is faster and a bit more precise.

Cheers,

Michael

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04-25-2016, 06:42 PM	#1
priyam21292 Junior Member Location: Memphis Join Date: Apr 2016 Posts: 1	Tophat Inner Mean Distance Hello all, I'm currently working on RNA-seq analysis using Galaxy. The dataset which I'm using is a paired-end data from BodyMap Project. For the BodyMap Project, inner mean distance of 110 is recommended for TopHat. I'm trying to put different values and see the results, but the results aren't as expected. If I'm right, I should be getting the best alignment with the recommended inner mean distance. In this case, I've tried 50, 110, 300 and 400. But there is not much difference in the alignment summary with the given set of input. Why is that?

04-26-2016, 12:29 AM	#2
Michael.Ante Senior Member Location: Vienna Join Date: Oct 2011 Posts: 123	Hi Priyam21292, TopHat estimates the mean inner distance itself. It uses - if given - the input value as a starting point for the optimisation. In case you provide this parameter, the computing is faster and a bit more precise. Cheers, Michael