- 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?
I wrote something about quantification considerations in the vignette of my R package IsoformSwitchAnalyzeR which might be relevant. TL;DR: you probably need to venture outside of R but those tools are really easy to use :-)
Rsubread and HISAT2 are both splice aware. All the RNA-seq aligners are splice-aware, otherwise they wouldn't be RNA-seq aligners.
I personally find Rsubread the fastest and easiest aligner for a gene-level differential expression analysis (but note I'm an Rsubread author).