I'm currently learning different approaches for RNA-seq data QC, alignment, and analysis. However, I'm confused that which tool is best for alignment. Because I'm comfortable with R, I'd rather stay in R environment and use Rsubread but I want to be sure that I'm not sacrificing accuracy for ease.
What do you think about Rsubread? How does it compare to other tools considering speed and accuracy? Is it splice-aware? How does it compare to HISAT2?