I ran HISAT2 to get alignments for the E5 Pocillopora data using the P. meandrina reference we had decided on here in the wiki. Overall alignment rates look kind of low. Are we sure about using this?
Alignment Summary
| Reads | Aligned concordantly 0 times | Aligned concordantly exactly 1 time | Aligned concordantly >1 times | Overall Alignment Rate |
|---|---|---|---|---|
| 54,219,233 | 24,674,401 (45.51%) | 24,699,780 (45.56%) | 4,845,052 (8.94%) | 64.15% |
| 51,579,450 | 24,586,231 (47.67%) | 22,163,871 (42.97%) | 4,829,348 (9.36%) | 60.90% |
| 55,302,459 | 26,420,392 (47.77%) | 26,136,411 (47.26%) | 2,745,656 (4.96%) | 62.04% |
| 53,353,608 | 26,586,350 (49.83%) | 24,622,354 (46.15%) | 2,144,904 (4.02%) | 60.58% |
| 42,513,488 | 25,177,347 (59.22%) | 16,194,243 (38.09%) | 1,141,898 (2.69%) | 50.59% |