I compared the counts per gene of summarizeOverlaps and HTSeq (python). The correlation was ~0.98. Although the correlation is very good, I was surprised that it was not roughly or equal 1, because summarizeOverlaps is according to the documentation designed after the counting modes in HTSeq (I use "Union" mode for both, Single end). The settings in both tools are the same.
While reading a bit more I came across the paper introducing "featureCounts". When they compared featureCounts with summarizeOverlaps and HTSeq in section 5.2, the results of summarizeOverlaps and HTSeq also slightly vary from each other.
My question now is, why summarizeOverlaps and HTSeq slightly vary. Unfortunately, I could not find further reading on the differences in the algorithm. So I assume that both tools are not the same, as I previously thought.
Thanks for some information!