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

________________________________ This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment.

The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system.

OCIMUMBIO SOLUTIONS (P) LTD