Question: Empty Cuffdiff Output
gravatar for wzaky
4.4 years ago by
United States
wzaky10 wrote:

What does empty Cuffdiff FRPKM empty files means? I was not able to run my RStudio for my Cuffdiff results, because of these empty cuffdiff outputs. 



rna-seq • 2.4k views
ADD COMMENTlink modified 4.4 years ago by Jennifer Hillman Jackson25k • written 4.4 years ago by wzaky10
gravatar for Jennifer Hillman Jackson
4.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:


This most likely means that you did not have the extra attributes included in your reference annotation file (GTF or GFF3) provided to Cufflinks and/or CuffMerge in an upstream step.

The tss_id and p_id attributes are factors here. Including gene_id will include the common gene name in the output, if provided in the annotation.

The Cufflinks web site has versions of annotation files with these attributes included for many common model organisms. Be sure to use the UCSC version, if using the same reference genome in Galaxy:

There can be other causes, that include genome mismatch problems (identifiers that do not match) but these result in other symptoms along with this one. If you think this may be a cause, the wiki help here can help:

Hopefully these resources help to diagnose your specific issue,

Jen, Galaxy team

ADD COMMENTlink written 4.4 years ago by Jennifer Hillman Jackson25k
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