I want to add support for paired-end reads in my ChIP-Seq software, which in itself is straightforward, but I came to think of a complication: the mappability should be much higher for PE reads. How do I deal with this? (MACS is another piece of software that handles paired-end reads, and I cannot see them mentioning it anywhere in their docs.)
It should be higher obviously, but how much?
These people claim to have come up with a solution:
Third, we investigate how the use of paired-end sequencing or mate-pair libraries relates to mappability. To this end, we predict and quantify how many of the pairs obtained from a typical DNASeq experiment can be rescued by taking advantage of the uniqueness of one of its reads and of the distance information for the pair.
I will have to look at their paper Fast Computation and Applications of Genome Mappability