Hi Wei,

Have a look at RNASeQC which provides more than what you specified here. 
This generates a detailed report with all relevant metrics on your RNA data.. I 
think, integrating this - a java based tool - into Galaxy should resolve your 

Hope this helps.


From: galaxy-user-boun...@lists.bx.psu.edu 
[mailto:galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Wei Liao
Sent: Friday, December 07, 2012 3:57 AM
To: galaxy-user@lists.bx.psu.edu
Subject: [galaxy-user] Tophat alignment statistics?

Hi, galaxy users

How to get Tophat alignment statistics such as % of reads aligned to exon, 
intron, splice junction? is there a Log file available?
How many unique and mutiple alignments?
I use Bam index, Flagstat, and Bam alignment metrix in Galaxy, but none 
reported the information I need.

Wei Liao
Research Scientist,
Brentwood Biomedical Research Institute
16111 Plummer St.
Bldg 7, Rm D-122
North Hills, CA 91343
818-891-7711 ext 7645

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