Do I need to assume differences in coverage profile when I compare the first reads from paired end data with single end read data?

Question

[corinna.ernst]

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!

Answer 1

[GenoMax]

Unless a significantly different library preparation method was used the first read from a paired-end library should be equivalent to a library that was sequenced only from one end.