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Question: Rnaseq For Solid Data
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gravatar for Di Kim Nguyen
7.3 years ago by
Di Kim Nguyen • 10
Di Kim Nguyen • 10 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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modified 7.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.3 years ago by Di Kim Nguyen • 10
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gravatar for Jennifer Hillman Jackson
7.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
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%2 0Quotas 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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
ADD COMMENT • link written 7.2 years ago by Jennifer Hillman Jackson ♦ 25k
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