Hi everyone,

I've done some RNA-seq on human cell lines and want to see the effect of synonymous codon usage in my two conditions. I've come to the conclusion that if I were to compare the SCU in my two conditions, I would have to normalize to mRNA abundance. Initially I used STAR (map to genome) and DESeq2 and then calculated the codon usage of the longest transcript of each gene (which I completely disagree with now).

I used RSEM, which the notes claims calculates expression levels of each transcript, but is excruciating slow (has been running for over a week even though I used 30 threads in my initial command - calculating confidence interval is the bottleneck from what I can tell).

Can anyone suggest a strategy where I would be able to accurately compare the SCU in my conditions?

Thanks in advance!