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
Hello, Some tests are running to determine if htseq-count is producing the correct input. This tool form is new to me as well, so am testing a few things out to see where the corner cases are that could trigger errors. Feedback from me early next week.
Thanks for the details here, very helpful. You usage case should work. But that is part of the test. If you can reproduce this at http://usegalaxy.org and want to submit a bug report (with a link to this post), that could be helpful if there are other minor input issues. If you do not actually have errror datasets, but rather "green" failure datasets, a shared history link sent to galaxy-bugs@lists.galaxyproject.org is another way to allow us to review. All datasets for review must be left undeleted. And it is best to not submit a very large history, as these are difficult to import. Just the inputs for this test (sam inputs, reference gff used, htseq-counts, then this tool's datasets).
Thanks, Jen, Galaxy team
sorry can't I use raw counts file coming from featurecounts???
Btw. why do you think this is an error? Is your dataset red? I can not see any error message in it, for me it looks like normal stdout messages about the design matrix.