Thank you for your suggestions JC.
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Transcript quantification using the reference transcriptome(gencode) and the raw RNA-Seq reads without mapping it to reference genome.
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?
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if the gene models are correct and you want only to quantify known genes, it is perfectly fine.
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