Question: How to incorporate quantile normalization within a pipeline?
gravatar for dragon28
2.0 years ago by
dragon2830 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
ADD COMMENTlink modified 2.0 years ago by Jennifer Hillman Jackson25k • written 2.0 years ago by dragon2830
gravatar for Jennifer Hillman Jackson
2.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:


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:

Best, Jen, Galaxy team

ADD COMMENTlink written 2.0 years ago by Jennifer Hillman Jackson25k
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