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Question: Missing CuffDiff results
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gravatar for m.plate
2.0 years ago by
m.plate • 0
m.plate • 0 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 • 601 views
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modified 2.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.0 years ago by m.plate • 0
0
gravatar for Jennifer Hillman Jackson
2.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

There were some server issues this morning at Galaxy Main http://usegalaxy.org. 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). https://wiki.galaxyproject.org/Support#Reference_genomes

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 COMMENT • link modified 2.0 years ago • written 2.0 years ago by Jennifer Hillman Jackson ♦ 25k
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