## Paired-end Data

When reads are paired, in order to perform statistics on pairs rather than on single reads, the read pairs have to be matched together. Reads without matching pair, or whose read mate aligns to a different chromosome, are excluded. The genomic positions given in the resulting table are equivalent to the respective actual DNA molecule that was sequenced from both ends.

The chromosome bar plot, specificity, enrichment and duplicate analysis (if selected) will be based on read pairs rather than on single reads.

      > readpairs <- reads2pairs(reads)

Number of read pairs: @NPAIRS@

Number of reads without matching second read, or whose second read aligns to a different chromosome: @NSINGLES@

Insert size histogram

Visualization of read pair insert sizes, i.e. the distances from the start of read 1 to the end of read 2, respectively.

      > insert.size.hist(readpairs)

@ISIZEHIST@