RNA-seq biological replicates for DGE

Question

[amy16]

I would like to know how you treat biological replicates for differential gene expression? So far, they have similar QC after trimming adapters and so I proceeded with alignment to reference genome, Now after the alignment I am not clear how to treat these biological replicates in the Differential gene expression.

Answer 1

[Devon Ryan]

The standard process is to determine per gene counts in each sample (e.g., with featureCounts) and load all of those into R (e.g., using DESeq2, edgeR, or limma/voom). You will not merge your replicates.