Table 1.
Statistics on the number of clusters for various clustering options compared to Corset
| Chicken | Human | Yeast | |||||
|---|---|---|---|---|---|---|---|
| Trinity | Oases | Trinity | Oases | Trinity | Oases | ||
| Contigs | 335,377 | 540,933 | 107,389 | 239,426 | 7,353 | 27,013 | |
| Trinity | Clusters (Max.) | 230,924 (302) | 73,258 (91) | 6,690 (45) | |||
| Oases | Clusters (Max.) | 87,639 (93,103) | 55,746 (16,881) | 3,140 (5,987) | |||
| CD-HIT-EST | Clusters (Max.) | 282,285 (81) | 202,636 (116) | 90,115 (29) | 96,965 (74) | 7,117 (8) | 5,586 (39) |
| Corset | Clusters (Max.) | 91,653 (290) | 67,826 (208) | 43,663 (90) | 38,476 (59) | 3,796 (45) | 4,324 (65) |
Shown are the number of contigs (bold), number of clusters and the maximum number of contigs in a cluster (in parentheses). Corset removes contigs that have less than 10 reads mapping to them by default, and hence has the least number of clusters in 5 out of 6 assemblies. This makes the final list of clusters more manageable, with no detriment to the final DGE results. Oases grossly over-clusters as shown by the maximum contigs in a cluster.