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Table 1 Statistics on the number of clusters for various clustering options compared to Corset

From: Corset: enabling differential gene expression analysis for de novoassembled transcriptomes

 

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)

  1. 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.