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Question: How to incorporate quantile normalization within a pipeline?
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gravatar for dragon28
2.0 years ago by
dragon28 • 30
dragon28 • 30 wrote:

Hi Biostars, How to perform quantile normalization in a pipeline on biostars? Is this done by cuffquant then cuffnorm? Or is this done automatically (eg. by cuffdiff)?

Thanks in advance
rna-seq tophat cufflinks galaxy • 521 views
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modified 2.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.0 years ago by dragon28 • 30
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gravatar for Jennifer Hillman Jackson
2.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Use the tool Cuffdiff. The tool form option is labeled Library normalization method.

The others two tools are optional and perform slightly different functions. See the manual for a description of each tool, option descriptions, and example pipelines. The Galaxy RNA-seq tutorial is also helpful: https://github.com/nekrut/galaxy/wiki/Reference-based-RNA-seq

Best, Jen, Galaxy team
ADD COMMENT • link written 2.0 years ago by Jennifer Hillman Jackson ♦ 25k
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