I have done the alignment with HISAT2 and then generated the FeatureCounts files. Then I tried to run Deseq2 to do the differentially expressed gene analysis for 6 samples (3 parental, 3 resistant). After about 10min running, I have seen the error message:
“Error in DESeqDataSet(se, design = design, ignoreRank) :
some values in assay are ne”