Differences of coverage within the same transcript

[liscruk]

Hi,

I was thinking about using the coverage as a surrogate for abundance and further analysis. However, I found it surprising that for some transcripts the difference in coverage over positions within the same transcript was quite strong.

Is this expected ?

I assumed that given these are full-length native mRNAs the coverage should not vary that drastically within modified positions or is this the coverage only computed for the individual kmer?

Here is one example:

symbol	position	coverage_KO.rep1	coverage_WT.rep1	ID	log2fc
ACTB	2122	140	104	ACTB-2122	4.288433e-01
ACTB	484	224	163	ACTB-484	4.586268e-01

Thanks for the help in interpreting this !

Best,