FAQ - Howto do RNA-seq Bioinformatics analysis on Galaxy

One of the top questions posted in the Galaxy User mailing list. 
reposted the summary links here for convenience.

Tutorial covering RNA-seq analysis (tool under "NGS: RNA Analysis")
http://usegalaxy.org/u/jeremy/p/galaxy-rna-seq-analysis-exercise

FAQ to help with troubleshooting (if needed):
http://usegalaxy.org/u/jeremy/p/transcriptome-analysis-faq

For visualization, an update that allows the use of a user-specified
fasta reference genome is coming out very soon. For now, you can view
annotation by creating a custom genome build, but the actual reference
will be not included. Use "Visualization -> New Track Browser" and
follow the instructions for "Is the build not listed here? Add a Custom
Build".

Help for using the tool is available here:
http://galaxyproject.org/Learn/Visualization 

Currently, RNA-seq analysis for SOLiD data is available only on Galaxy test server:
http://test.g2.bx.psu.edu/

Please note that there are quotas associated with the test server:
http://galaxyproject.org/wiki/News/Galaxy%20Public%20Servers%20Usage%20Quotas


[Credit : Jennifer Jackson ]
http://usegalaxy.org
http://galaxyproject.org/Support


Another helpful resource (non-Galaxy related though) is
http://seqanswers.com/wiki/How-to/RNASeq_analysis written by Matthew Young
and the discussion on this wiki @ seqanswers
http://seqanswers.com/forums/showthread.php?t=7068

As well as this review paper in Genome Biology RNA-seq Review

Stephen mentions this tutorial as well in this blog

Dr David Matthews has posted a starter thread to discuss RNA seq analysis workflow on Paired End Seq with Tophat on Galaxy in the mailling list.

RNA seq analysis workflow on Galaxy (Bristol workflow)

His post and the discussion thread is here.
http://gmod.827538.n3.nabble.com/Replicates-tt2397672.html#a2560404 

kevin:waiting for the next common question to come next, is there Ion Torrent Support on Galaxy ?)