Hi Wei,

 

Have a look at RNASeQC which provides more than what you specified here. (https://confluence.broadinstitute.org/display/CGATools/RNA-SeQC)

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 problem.

 

Hope this helps.

 

Raj

 

From: galaxy-user-bounces@lists.bx.psu.edu [mailto:galaxy-user-bounces@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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