RNA-Seq quantification methods

Question

[Chris]

Hi all,

In RNA-Seq, there are two ways of quantification:

• using a reference genome
• directly on the transcriptome
  I read about that but I still don't understand the second way. Would anyone can give an easy-to-understand material or you can explain it here?

Thank you so much!

https://combine-lab.github.io/salmon/getting_started/

[grant.hovhannisyan]

what exactly you don't understand - the methodological details or the general idea?

[Chris]

The general idea. It is quite hard for me to understand this if just Googling.

[grant.hovhannisyan]

there are many threads about this in biostars - for example take a look here Alignment and mapping or here Could you explain the difference between STAR, KALLISTO, SALMON etc. to experimental Biologist/non-bioinformatician