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Question: Empty Cuffdiff Output
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gravatar for wzaky
4.4 years ago by
wzaky • 10
United States
wzaky • 10 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
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modified 4.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.4 years ago by wzaky • 10
0
gravatar for Jennifer Hillman Jackson
4.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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. 
http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff_input

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: http://cufflinks.cbcb.umd.edu/igenomes.html

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

Hopefully these resources help to diagnose your specific issue,

Jen, Galaxy team
ADD COMMENT • link written 4.4 years ago by Jennifer Hillman Jackson ♦ 25k
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