Question: Missing CuffDiff results
gravatar for m.plate
14 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 • 307 views
ADD COMMENTlink modified 14 months ago by Jennifer Hillman Jackson23k • written 14 months ago by m.plate0
gravatar for Jennifer Hillman Jackson
14 months ago by
United States
Jennifer Hillman Jackson23k 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 14 months ago • written 14 months ago by Jennifer Hillman Jackson23k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 117 users visited in the last hour