Hi,

I'm looking for any technical information regarding how subread-align distinguishes properly paired from not-properly paired alignments for paired-end data (example summary below). I've looked through the subread/Rsubread documents and not found it (although I could have missed it).

Further, if anyone has experience aligning reads to a congener species assembly with subread and suggestions for parameter optimization, input would be greatly appreciated.

Thanks!

    //================================   Summary =================================\\
    ||                                                                            ||
    ||             Total fragments : 12,563,751                                   ||
    ||                      Mapped : 8,918,955 (71.0%)                            ||
    ||             Uniquely mapped : 8,918,955                                    ||
    ||               Multi-mapping : 0                                            ||
    ||                                                                            ||
    ||                    Unmapped : 3,644,796                                    ||
    ||                                                                            ||
    ||             Properly paired : 5,290,912                                    ||
    ||         Not properly paired : 3,628,043                                    ||
    ||                   Singleton : 2,281,674                                    ||
    ||                    Chimeric : 80,494                                       ||
    ||       Unexpected strandness : 25,231                                       ||
    ||  Unexpected fragment length : 1,225,432                                    ||
    ||       Unexpected read order : 15,212                                       ||
    ||                                                                            ||
    ||                      Indels : 145,958                                      ||
    ||                                                                            ||
    ||                Running time : 7.7 minutes                                  ||
    ||                                                                            ||
    \\============================================================================//
See arguments `minFragLength`, `maxFragLength` and `PE_orientation`. I think "Properly paired" means that both ends map to the same chromosome with the expected orientation and the fragment defined is within the expected length range.