Table 1 Evaluation of the scaffolding using the Trinity-assembled transcripts.

From: Improvement of genome assembly completeness and identification of novel full-length protein-coding genes by RNA-seq in the giant panda genome

 

Transcripts

Scaffold

Connection

++1

−−1

+−/−+1

Total

OK_join2

499

2,195

2,083

4,777

1,205

741

OK_merge3

56

47

95

198

152

79

PB_merge4

605

589

1,269

2,463

987

1,503

Total

1,160

2,831

3,447

7,438

2,106

2,317

  1. 1The mapping strands of two ordinal, aligned segments resulted in transcripts located across multiple scaffolds, which were oriented ‘+/+’, ‘−/−’, or ‘+/−’.
  2. 2OK_join: the Trinity-assembled transcript alignment results suggested that these scaffold sequences were adjacent, which was used to improve scaffolding.
  3. 3OK_merge: the Trinity-assembled transcript alignment results suggested that the most likely situation was that one genomic sequence filled the gap in another.
  4. 4PB_merge: the Trinity-assembled transcript alignment results suggested that mis-assembly existed within these scaffolds/contigs.
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