Question: Using Cufflinks v. 2.2.1.5
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gravatar for gkuffel22
4 months ago by
gkuffel22170
United States
gkuffel22170 wrote:

Hello community,

Let me lead with, I have never been able to successfully run the tophat2-cufflinks-cuffmerge-cuffdiff pipeline before and actually end up with non-zero values populated in the log-fold change column AND get gene names as I show a screenshot below, so as you can imagine it is a good day. With that said, for some reason eventhough the tool completes successfully and seemingly the data is intact the jobs in my local Galaxy finish red, as if an error has occurred. When I click on the little bug to view the error, there is no error message listed, just info about the job processing. Does anyone know why this is happening?

gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant XLOC_000001 XLOC_000001 thrL Chromosome:189-255 Control Treatment NOTEST 0 0 0 0 1 1 no XLOC_000002 XLOC_000002 thrA Chromosome:336-2799 Control Treatment OK 160.894 10.862 -3.88875 -9.15771 5e-05 0.000153368 yes XLOC_000003 XLOC_000003 thrB Chromosome:2800-3733 Control Treatment OK 154.107 33.7264 -2.19198 -5.07483 5e-05 0.000153368 yes

ADD COMMENTlink modified 4 months ago by Martin Čech ♦♦ 4.0k • written 4 months ago by gkuffel22170
0
gravatar for Martin Čech
4 months ago by
Martin Čech ♦♦ 4.0k
United States
Martin Čech ♦♦ 4.0k wrote:

Generally Galaxy datasets turn red when the tool writes anything into stderr during the job run. This output should be available if you click the (i) icon on the dataset.

ADD COMMENTlink written 4 months ago by Martin Čech ♦♦ 4.0k
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