I just ran my first successful (I think) DNA alignment operation with `bowtie2` on some paired end data (namely SRR390728) and these were the results I got:
7178576 reads; of these: 7178576 (100.00%) were paired; of these: 7177909 (99.99%) aligned concordantly 0 times 225 (0.00%) aligned concordantly exactly 1 time 442 (0.01%) aligned concordantly >1 times ---- 7177909 pairs aligned concordantly 0 times; of these: 1624832 (22.64%) aligned discordantly 1 time ---- 5553077 pairs aligned 0 times concordantly or discordantly; of these: 11106154 mates make up the pairs; of these: 1231919 (11.09%) aligned 0 times 1884213 (16.97%) aligned exactly 1 time 7990022 (71.94%) aligned >1 times 91.42% overall alignment rate
So my first impression was "WOOOOO!!! AWESOME", but on further inspection I saw:
7177909 (99.99%) aligned concordantly 0 times
And so my second impression was "hmmmm.......", and now here I am. From the Bowtie 2 manual I found that:
- "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"."
Now I'm confused about how this information applies to my data. Should I interpret this as a problem with my dataset? Is my alignment reliable? What else should this lead me to consider?