Question: Using DESeq2 inside Galaxy
gravatar for Marcelo Pereira
14 months ago by
Marcelo Pereira70 wrote:


I have been trying to use DESeq2 on Galaxy, and am having issues with this package.

To illustrate the problem, I have 6 datasets (T1, T2, T3, C1, C2, and C3), being T the treatment samples, and C the control samples.

Here are examples of the content of each sample (I am showing the first lines of T1 and C1 only, but the other datasets are all similar):

gene1   331
gene2   74
gene3   50
gene4   1676.27
gene5   496.99
gene6   0

gene1   361
gene2   59
gene3   30
gene4   1906
gene5   639
gene6   12

In the package DESeq2 1.8.2 on Galaxy, I am using the following arguments:

  • Factor:  Treatment
  • 1: Factor Level:  Treated
    • Count Files: T1, T2, T3
  • 2: Factor Level:  Control
    • Count Files: C1, C2, C3

Then I got the following error:

DESeq2 run information

sample table:
dataset_1.dat     Treated
dataset_2.dat     Treated
dataset_3.dat     Treated
dataset_4.dat     Control
dataset_5.dat     Control
dataset_6.dat     Control

design formula:

primary factor: Treatment


I couldn't find the documentation on how to use the Galaxy package DESeq2, and I am not sure about the format of the input files.

Has anyone successfully used DESeq2 inside Galaxy? Could you please let me know how your inputs look like, or if you have any info on how to properly use this package?



ADD COMMENTlink modified 13 months ago by Michael Love11k • written 14 months ago by Marcelo Pereira70

hi Marcelo,

I can't help so much here, although I helped with the R script, I don't know what could be the problem.

Did you actually paste in an error here? I don't see anything looking like error text.

You might also want to ping the Galaxy wrapper authors to this thread, if you don't hear any other feedback.

ADD REPLYlink written 14 months ago by Michael Love11k

FIXED the problem.  It was a simple fix, and I apologize for bothering the list with such type of problem.

The issue was on how Galaxy was importing the data.  I didn't notice it was loading the dataset without properly setting separated columns for the gene name and the expression level.  Each line had only one column (instead of two), in which the gene name and the expression level was merged.

After properly importing the datasets, and making sure the columns were set, the package DESeq2 on Galaxy worked great.


ADD REPLYlink written 13 months ago by Marcelo Pereira70

Hi Marcelo,

I had the same problem with DESeq inside Galaxy. May you give an example of the right file format?



ADD REPLYlink written 9 months ago by domenico.depaola0
gravatar for Michael Love
13 months ago by
Michael Love11k
United States
Michael Love11k wrote:

OP fixed: C: Using DESeq2 inside Galaxy

ADD COMMENTlink written 13 months ago by Michael Love11k
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