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Question: cuffdiff not properly working
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gravatar for sawabe
2.9 years ago by
sawabe • 0
sawabe • 0 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.

best

Tomoo Sawabe

 

 

 

 

   
cufflinks • 532 views
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modified 2.9 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.9 years ago by sawabe • 0
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gravatar for Jennifer Hillman Jackson
2.9 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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: https://wiki.galaxyproject.org/Support#Reference_genomes

Thanks, Jen, Galaxy team
ADD COMMENT • link written 2.9 years ago by Jennifer Hillman Jackson ♦ 25k
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