Question: Transcript quantification using the reference transcriptome(gencode) and the raw RNA-Seq reads without mapping it to reference genome.
gravatar for Glory Basumata
14 months ago by
India/Guwahati/Indian Institute of Technology Guwahati
Glory Basumata140 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 14 months ago by JC10k • written 14 months ago by Glory Basumata140
gravatar for JC
14 months ago by
JC10k wrote:

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

ADD COMMENTlink written 14 months ago by JC10k

Thank you for your suggestions JC.

ADD REPLYlink written 14 months ago by Glory Basumata140
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