Hello,
Currently, RNA-seq analysis for SOLiD data is available only on our 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%20Qu...
Should you require additional resources, then it would be necessary to
create a local or cloud instance:
http://galaxyproject.org/wiki/Big Picture/Choices
The basic steps are to prepare the fastq data then proceed with mapping
and analysis.
Please see the screencasts specific to SOLiD data to prepare the input
fastq file(s). Once the initial steps are completed, move on to the
tutorial below (TopHat mapping, etc.):
http://main.g2.bx.psu.edu/u/aun1/p/ngs-analysis-service
http://galaxyproject.org/wiki/Learn/Screencasts
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
Hopefully this helps,
Best,
Jen
Galaxy team
On 8/31/11 4:28 PM, Di Kim Nguyen wrote:
Hi,
I needed help in crunching RNA-seqs done with solid platform. I have
fasq files. Please give me the steps necessary in this process to get
the fpkm from cufflink? This is mouse data.
Thank you very much, please accept my appreciation.
Di Nguyen
U of Washington
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