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.
[mailto:galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Wei Liao
Sent: Friday, December 07, 2012 3:57 AM
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.
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
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
To manage your subscriptions to this and other Galaxy lists,
please use the interface at: