From transcript to gene - Salmon quantification

Question

[JulianC]

Hi!

I am working with Salmon to quantify gene expression from single-cell RNA-seq data. I used NCBI transcriptome (in FASTA format; https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/635/GCF_000001635.26_GRCm38.p6/GCF_000001635.26_GRCm38.p6_rna.fna.gz) as index, and my quantification went pretty well. The output gave me TPM values for each transcript. For example, for a gene with three transcripts, I end up with three different quantifications, one for each transcript. Since I want to have a gene-specific quantification, is it fair to sum up the TPM values of the three transcripts to obtain one single quantification relative to that gene? Thank you in advance!

Answer 1

[ATpoint]

Basically yes, but there is dedicated software for this. I suggest you use tximport to summarize the transcript level estimates to the gene level. This on the one hand provides you with gene level counts and on the other hand calculates the average and sample-specific length for each gene depending on which transcripts/isoforms contribute to the gene level count. The tximport vignette and paper discusses details.