Question: Transcript quantification using the reference transcriptome(gencode) and the raw RNA-Seq reads without mapping it to reference genome.
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gravatar for Glory Basumata
9 days ago by
India/Guwahati/Indian Institute of Technology Guwahati
Glory Basumata10 wrote:

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?

ADD COMMENTlink modified 9 days ago by JC7.6k • written 9 days ago by Glory Basumata10
1
gravatar for JC
9 days ago by
JC7.6k
Mexico
JC7.6k wrote:

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

ADD COMMENTlink written 9 days ago by JC7.6k

Thank you for your suggestions JC.

ADD REPLYlink written 6 days ago by Glory Basumata10
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