mRNA production relation to gene length in RNASeq

Question

[Abhishek]

Hi all,

I'm trying to understand this normalization method comparison study : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6171491/

In Fig 2, B) it is mentioned -

Within each condition, the two genes produce the same amount of mRNA (in bp) but gene 2 is four-fifth the length of gene 1, so must produce five-fourth the number of molecules that gene 1 does.

I don't really understand this. From my understanding, if gene2 is 4/5 length of gene 1, it should produce 4/5 number of molecules compared to gene1.

Please help me understand this.

Answer 1

[ATpoint]

In full-length RNA-seq, given two genes have same expression level, then there is indeed a correlation between counts and length, as longer genes produce more fragments. This of course assumes that all fragments can be sequenced the same, like PCR/GC/mappability-bias was not existing which is of course not true, so this statement is an approximation, not a precise reality, like everything in biology. Maybe this sentence above is a typo, so if a gene is 20% shorter it should roughly produce 20% fewer reads, given expression level was similar.