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%20Quota...

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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