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 ||
|| ||
\\============================================================================//
1 answer
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.
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