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 ?) 

Pauline Ng expects a genome analysis to cost $500.

Pauline Ng is planning open source, open access analytics for the genomes to come.

By Allison Proffitt

August 2, 2011 | SINGAPORE—Pauline Ng’s office is the Genome building of the Biopolis science park in Singapore, a fitting home for one of the authors of the first published personal genome, that of J. Craig Venter, published in 2007 while Ng was a senior scientist at the J. Craig Venter Institute.

Now Ng leads an expanding group of three bioinformaticists (she’s hiring!) at the Genome Institute of Singapore (GIS). Before her stint at the Venter Institute, Ng worked for Illumina as well as the Fred Hutchinson Cancer Center in Seattle, where she wrote the powerful SIFT algorithm (http://sift-dna.org), a widely used tool to predict the effect of a given amino acid substitution on protein function. 

But sequencing and analysis—today at least—cost the same. “The problem is that right now, companies like Knome are actually charging the same amount for bioinformatics as they are for sequencing. If you sequence more individuals, I’d expect the bioinformatics to go down, but it’s the same price. That means the price is double! If we can make these tools online, accessible for free or at least at cost, I think I can get it to a tenth of the cost.”

Ng plans to do the computation on the Amazon Cloud and, at today’s rates, expects a genome analysis to cost $500. She hopes that these price points will enable doctors and individuals to use genomics. “If we could say, OK, outsource [the sequencing] to these companies. You’re going to get a hard disk. Mail it to Amazon and get your results in a week.”

Ng is not promising a magic cure, and doesn’t even think that this model should be the only one. She just hopes to drive prices down and open the market. “There’s never a guarantee of an answer,” she says. “Even with the software we write, there may not be a guarantee of an answer, but at least…” she pauses and begins again, emphatically. “We can definitely give you the basic annotation and provide the tools that everyone uses. And if it doesn’t work, then you go to an expensive company that really uses the same tools as the academics but with a couple of more bells and whistles. If you try our stuff first, at least you’ve invested only $500 instead of $5,000.” 

Full article here

Dleon highlights tools worth a mention at ABRF 2010

from Dleon

Some of these are new to me as well!

excerpt
GNomEx:
It is a a web accessible database and LIMS to organize and track the generation of raw genomic data and associated downstream analysis.
https://hci-as1.hci.utah.edu/gnomex/gnomex.html

GenoPub:
It is a Genomic Annotation Publisher which stores information about each annotation in a database. http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2

Intergrative Genome Browser:
The Integrated Genome Browser is an interactive, zoomable, scrollable software program you can use to visualize and explore genome-scale data sets, such as tiling array data, next-generation sequencing results, genome annotations, microarray designs, and the sequence itself.
http://www.bioviz.org/igb/

Galaxy:
Galaxy allows you to do analyses without the need to install or download software. You can analyze multiple alignments, compare genomic annotations, profile metagenomic samples, etc.
http://main.g2.bx.psu.edu/

The First Galaxy Developer Conference 2010

The First Galaxy Developer Conference will be in May. I am quite excited and hope to attend if I can.

p.s. I totally love how they capitalise the most important parts of the conference. BEER and FOOD