Subread-align: Properly-paired versus not properly paired

Question

[rependo]

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                                  ||
||                                                                            ||
\\============================================================================//

Answer 1

[Gordon Smyth]

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.

[rependo]

Many thanks, Gordon.