Question: Error in DESeq2
0
gravatar for encarnaciona
6 months ago by
encarnaciona20
encarnaciona20 wrote:

Hello,

I'm trying to run a DESeq2 analysis of my ten RNASeq Samples. I successfully was able to use the htseq analysis for these, generating one file with counts and one file listed as (no feature) for each of the 10 samples. From there I've been trying in vain to do DESeq2.

I name the factor and have tried setting Factor 1 as Control and Factor 2 as Treatment and viceversa. I keep everything as default save normalizing the outliers, and select all my treatment and control groups for analysis including the no feature groups. I keep receiving a data set error, where the Factor 2 data sets regardless of being control or treatment seem to have a problem.

An error occurred with this dataset: DESeq2 run information

sample table:

                 HSP12OEXRNASeq

dataset_24012997.dat Control

dataset_24012998.dat Control

dataset_24013002.dat Control

dataset_24013004.dat Control

dataset_24013010.dat Control

Any ideas? Thanks in advance!

rna-seq deseq2 • 295 views
ADD COMMENTlink modified 6 months ago by n.goue50 • written 6 months ago by encarnaciona20
1
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Only input the primary htseq-count output datasets. Avoiding the "no feature" datasets, those are extra log files, not data files.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 6 months ago by Jennifer Hillman Jackson25k

Thank you so much, Jennifer!

ADD REPLYlink written 6 months ago by encarnaciona20
1
gravatar for n.goue
6 months ago by
n.goue50
n.goue50 wrote:

Hi,

There is a nice tutorial to help you with HTseq and DeSeq2 you might know about ? http://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/rb-rnaseq/tutorial.html

Good luck!

ADD COMMENTlink written 6 months ago by n.goue50

Thank you; I actually hadn't seen that link!

ADD REPLYlink written 6 months ago by encarnaciona20
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