I got my mate pair run done, and I asked for a jump size of 3kb.
When I map my mate pairs against assembled contigs, I see that there are indeed mate pairs with sizes close to 3kb, but also a lot of reads that do not have any partner in the middle of an 100kb contig.
Is this common, that there are paired-end reads, with a size of 300bp, and a lot of single ended reads in a mate pair library? Is there any way to deal with this? It is confusing my assemblers and I am not getting bigger contigs by adding my mate pairs in.