Transcript quantification using the reference transcriptome(gencode) and the raw RNA-Seq reads without mapping it to reference genome.

Question

[Glory Basumata]

I am just curious to know how accurate would be the transcript quantification of the RNA-Seq reads using tools like Sailfish/Salmon without using the mapping tool like HISAT or STAR. Basically, I want to skip the mapping/aligning of the reads to it's reference genome and focus on isoform abundance study. Is this a good approach for transcript abundance study in eukaryotes?

Answer 1

[JC]

if the gene models are correct and you want only to quantify known genes, it is perfectly fine.

[Glory Basumata]

Thank you for your suggestions JC.