I am considering feeding paired-end sequencing data into a bioinformatics workflow for coverage profiling which is actually adapted to single-end reads. So my plan is to use only the first reads as input.
My question now is whether I have to assume systematic differences in the resulting coverage (given identical read lengths), or whether I can expect that the coverage resulting from single-end reads and the first read from PE data are comparable in principle. Does anyone have experience with this?
Many thanks in advance!