Question: cuffdiff-quartile normalization method
gravatar for raj_262920
3.8 years ago by
raj_26292020 wrote:


Why does the quartile normalization method does not produce any FPKM values for my data with the reference genome ( and 'NOTEST' for all the values) whereas geometric method produce many FPKM values and identifies significance?

What does that mean ? What is the difference and is it really significant ?


rna-seq galaxy • 1.9k views
ADD COMMENTlink modified 3.8 years ago by Jennifer Hillman Jackson25k • written 3.8 years ago by raj_26292020
gravatar for Jennifer Hillman Jackson
3.8 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The "NOTEST" result from Cuffdiff indicates that there was not enough data to perform the calculation. It could be that your data is shallow? Double check the mapping rates/jobs if this does not seem to be a good explanation for your particular inputs/reference genome and annotation.

Not infrequently, poor mapping rates can be traced all the way back to the quality score scaling of the input fastq data. If you wish to double check your fastq data, this wiki can help show you how:

For more detail, "NOTEST" is defined here in the manual:

For help in understanding the different "Library Normalization" (–library-norm-method) methods, please see the descriptions at: ->

Hopefully this helps, Jen, Galaxy team

ADD COMMENTlink written 3.8 years ago by Jennifer Hillman Jackson25k
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