Question: Missing CuffDiff results
gravatar for m.plate
16 months ago by
m.plate0 wrote:

Hi, I ran CuffDiff using genecode.v25annotation.gtf (downloaded from Gencode) as transcript GTF file. However when I look at the outputs, all the following files are empty:

  • splicing_differential_expression_testing
  • promoters_differential_expression_testing
  • CDS_overloading_diffential_expression_testing
  • CDS_FPKM_differential_expression_testing
  • CDS_FPKM_tracking
  • TSS_groups_differential_expression_testing
  • TSS_groups_FPKM_tracking

The remaining output files appear to be fine. Could someone please kindly tell me what I am doing wrong? I thought it might be the genecode .gtf file but after looking at it and looking at similar files used by other people to do similar analysis the file seems fine.

Thanks to anyone who can help me with this. Manu

rna-seq galaxy output cuffdiff • 355 views
ADD COMMENTlink modified 16 months ago by Jennifer Hillman Jackson24k • written 16 months ago by m.plate0
gravatar for Jennifer Hillman Jackson
16 months ago by
United States
Jennifer Hillman Jackson24k wrote:


There were some server issues this morning at Galaxy Main Your problem wouldn't be expected, but you could try a rerun anyway to make certain it is not related.

Apart from that, I suggest checking your inputs. The input BAM datasets have alignment content and were generated with Tophat, the same exact reference genome was used for each mapping and any intermediate steps, and that same reference genome is a match for the reference annotation (GTF).

If you are working somewhere else, and the above does not help to resolve the issue, contacting the administrators of the instance is the next step.

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 16 months ago • written 16 months ago by Jennifer Hillman Jackson24k
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