4. GS De Novo Assembler and GS Reference Mapper Appendices
:
4.8 Paired End Libraries in the 454 Sequencing System
: 4.8.4 True Pairs and False Pairs
4.8.4
True Pairs and False Pairs
“True Pairs” follow the normal rules for Paired End reads, i.e. they are within the expected library distance from each other, map to the same reference sequence or align within the same assembled contig or scaffold, and map or align in opposite orientations.
False Pairs are Paired End reads whose ends either:
•
map to different reference sequences or align in contigs that are in different scaffolds
•
map to locations on a single reference sequence or assembled contig with a distance outside the expected library span
•
have an unexpected relative orientation
