Question: error message when running Deseq2 on featureCounts output files
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yelekley7 • 0 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<-.data.frame`(`*tmp*`, value = value) :
duplicate 'row.names' are not allowed
Calls: rownames<- ... rownames<- -> row.names<- -> row.names<-.data.frame
Warning message:
non-unique value when setting 'row.names': 'RNA.STAR.on.data.38..data.4..and.others..mapped.bam'
Thanks
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.