Hi, this could be the general question regarding differential gene expression analysis.
Method 1: Mapping with STAR/HISAT2, counting the reads with HTSEQ, then DSEQ2.
Method 2: Count without alignment with Salmon and DESEQ2.
I usually do with the traditional method 1. But when I am comparing the two methods, getting about more than 60 percent differentially expressed genes? Did anyone experience that, or Did anyone do the same as I? What could be the potential reason for this difference?