Hello,
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):
T1
gene1 331
gene2 74
gene3 50
gene4 1676.27
gene5 496.99
gene6 0
...
C1
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:
Treatment
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:
~Treatment
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?
Thanks,
Marcelo
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.
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.
Thanks
Hi Marcelo,
I had the same problem with DESeq inside Galaxy. May you give an example of the right file format?
Thanks
Domenico