Question: cuffdiff not properly working
gravatar for sawabe
2.9 years ago by
sawabe0 wrote:

Thank you very much for providing the excellen project to use bioinfomatics.

I would like to analyse differentially expressed genes using cuffdiff, but it was unlikely to be working properly. Especially, CDS using gff file was not recognized. local cuffdiff program using the same gff was no problem. Could you please advise for me to fix this problem.


Tomoo Sawabe






cufflinks • 532 views
ADD COMMENTlink modified 2.9 years ago by Jennifer Hillman Jackson25k • written 2.9 years ago by sawabe0
gravatar for Jennifer Hillman Jackson
2.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:


This situation can occur when there is a genome mismatch between the inputs.

The GFF3/GTF reference annotation must be from the same exact genome build as the reference genome used for prior mapping steps. This includes exactly the same chromosome sequence identifiers in all inputs. Any differences and the annotation will be ignored.

This is how to verify the inputs:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.9 years ago by Jennifer Hillman Jackson25k
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