Hi,

I am running my bulk RNA-seq analysis, I use feature counts from subread package to generate my raw counts from bam files using paired-end option. Do I still need to give library type when I use DESeq() function to get my DEGs?

I appreciate your help!

The vignette includes that in the design because the example is a mix of single and paired end reads, and that is added to the design so that differences caused by the difference in library type can be modeled.

If all your samples are paired end, you don't have to include that in the design. You won't be using that information to determine DEGs.