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Table 1 Comparison of transcriptome assembly statistics

From: Do novel genes drive morphological novelty? An investigation of the nematosomes in the sea anemone Nematostella vectensis

 

Trimmed only, N = 3 reps/tissue

Trimmed only, N = 1 rep/tissue

Trim + error correction, N = 1 rep/tissue

Transcriptome name

TR333942

TR118377

NvecRef32743

Assembled “transcripts”a

333,942

118,377

32,743

Transcripts with predicted ORFsb

29,690 (9 %)

19,461 (16 %)

17,346 (53 %)

Predicted ORFsc

135,213 (4.6X)

77,877 (4X)

27,511 (1.6X)

ORFs with no expressiond

74,503 (55 %)

28,975 (37 %)

10,198 (37 %)

CEGMA score (complete) e

242/248 (98 %)

241/248 (97 %)

207/248 (83 %)

CEGMA score (partial)

245/248 (99 %)

245/248 (99 %)

231/248 (93 %)

  1. aTotal number of contigs assembled using Trinity [49, 50]. bOpen reading frames (ORFs) ≥ 100 amino acids (aa) in length were predicted using Transdecoder (http://transdecoder.github.io). cThe average number of ORFs predicted from each transcript is listed in parentheses. dTotal number of transcripts with at least one ORF and abundance estimated at < 2 counts in at least one of the three sampled tissues; counts were assayed using Bedtools [55]. eCEGMA scores are listed as % of the 248 conserved eukaryotic genes that form the CEGMA database [56] that were present in the indicated transcriptome (scores for complete and partial sequences are indicated)