hisat2 output from paired en reads.

Question

[Palgrave]

Can someone explain the difference between 571 (46.35%) aligned exactly 1 time and 8823 (88.23%) aligned concordantly exactly 1 time in the hisat2 output?

10000 reads; of these:
  10000 (100.00%) were paired; of these:
    650 (6.50%) aligned concordantly 0 times
    8823 (88.23%) aligned concordantly exactly 1 time
    527 (5.27%) aligned concordantly >1 times
    ----
    650 pairs aligned concordantly 0 times; of these:
      34 (5.23%) aligned discordantly 1 time
    ----
    616 pairs aligned 0 times concordantly or discordantly; of these:
      1232 mates make up the pairs; of these:
        660 (53.57%) aligned 0 times
        571 (46.35%) aligned exactly 1 time
        1 (0.08%) aligned >1 times
96.70% overall alignment rate

Answer 1

[Zhilong Jia]

Concordant pairs match pair expectation, discordant pairs don't : 8823 (88.23%) aligned concordantly exactly 1 time

A pair that aligns with the expected relative mate orientation and with the expected range of distances between mates is said to align "concordantly". If both mates have unique alignments, but the alignments do not match paired-end expectations (i.e. the mates aren't in the expected relative orientation, or aren't within the expected distance range, or both), the pair is said to align "discordantly". Discordant alignments may be of particular interest, for instance, when seeking structural variants.

The rest of the reads either align as singles or may not align at all. So the reads that are in this section is Total -(Concord.+Discord.). 571 (46.35%) aligned exactly 1 time

ref:

• http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#concordant-pairs-match-pair-expectations-discordant-pairs-dont
• amitm's reply in http://seqanswers.com/forums/showthread.php?t=21333

Answer 2

[ATpoint]

http://daehwankimlab.github.io/hisat2/manual/

By default, hisat2 looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior.