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?