Hi How does one work with coverage on GappedAlignmentPairs in the context of RNASeq? The simplest way is to consider each left and right read as separate - essentially loose the "paired" information and calculate coverage. However, if both the left and right pair reads fall within a feature of interest - say an exon, does it imply coverage of the region of the exon between the reads too >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LLLLLLLLLL---------------------------RRRRRRRRRR ^^^^^^^^^^^^^^^^^ In the figure above, the exon is represented by ">" and L and R represents the left and right reads aligned to the exon. I am talking about the region represented by "^". Do we assume coverage for this region too? Does Coverage on GappedAlignmentPairs do this? -best -Lax Center for Neuroscience Research Tufts Univeristy School of Medicine Boston, MA [[alternative HTML version deleted]]