Question: error message when running Deseq2 on featureCounts output files
gravatar for yelekley7
5 months ago by
yelekley70 wrote:

I get the following error message when running Deseq2 on two samples (tumor and normal) that was processed with STAR then with FeatureCounts. Please suggest how to correct the error.

Fatal error: An undefined error occurred, please check your input carefully and contact your administrator.
Error in `row.names<`(`*tmp*`, value = value) : 
  duplicate 'row.names' are not allowed
Calls: rownames<- ... rownames<- -> row.names<- -> row.names<
Warning message:
non-unique value when setting 'row.names': ''


rna-seq • 307 views
ADD COMMENTlink modified 4 days ago by Flow100 • written 5 months ago by yelekley70

You're probably using a dodgy GTF file that has duplicates for whatever reason.

Import a GTF file. Get data > UCSC main > select your model organism and under table select "refFlat". Try re-running FeatureCounts with that.

ADD REPLYlink written 4 months ago by VY120
gravatar for Flow
4 days ago by
Flow100 wrote:

Hey, I made a recent post about that error which you can find here. Maybe that helps.

ADD COMMENTlink written 4 days ago by Flow100
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