Go Back   SEQanswers > General

Similar Threads
Thread Thread Starter Forum Replies Last Post
Inner distance value for TopHat / Proper mapping with RNA-Seq PE data ocs Bioinformatics 6 11-27-2011 11:10 AM
TopHat Error: you must set the mean inner distance between mates with -r? xhuister Bioinformatics 2 02-24-2011 09:07 AM
tophat -r mate inner distance option ssseq Bioinformatics 2 01-10-2011 06:15 AM
Tophat mean inner distance error for SOLID data repinementer Bioinformatics 0 10-28-2010 07:58 PM
tophat -r mate inner distance mgogol RNA Sequencing 0 09-11-2009 02:41 PM

Thread Tools
Old 04-25-2016, 06:42 PM   #1
Junior Member
Location: Memphis

Join Date: Apr 2016
Posts: 1
Default 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?
priyam21292 is offline   Reply With Quote
Old 04-26-2016, 12:29 AM   #2
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.


Michael.Ante is offline   Reply With Quote

galaxy, inner mean distance, tophat

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 02:52 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO