I want to focus on transcriptome analysis. We know it's possible to analyze RNA-Seq experiment based on alignment or k-mers.Possible alignment workflow:Align sequence reads with TopHat2Quantify the gene expression with CufflinksPossible reference-free workflow:Quantify sequence reads with Kallisto reference-free indexBoth strategy generate gene expression table.Q: What are pros and cons for each of the approach? Can you give guideline?
Alignment based vs reference-free (transcriptome analysis)?
transcriptome;rna seq