If we had an insert length of 426bp and an adapter size of 65bp, then the length of the central region between two 100bp reads would be 96bp (426bp - 130bp - 100bp - 100bp).
So providing the mean length of reads in the library is in fact 100bp, then the avg. distance between the reads for that library would be 96bp.
As Istvan noted (https://www.biostars.org/p/112228/ ), if you were to trim off a fixed number of bases, for example resulting in an avg. read length of 98bp then presumably this distance would increase to 100bp.
If this increase in distance is correct, then how is it any different if we assume those removed bases were actually errors?
The 100bp read length is being reduced to 98bp so you would assume that the reads would map to a reference genome with 4bp more in-between them. Should I therefore find the average post-trimming read length of the library and use this to calculate the inner distance, or am I missing something here?
Thanks