Skip to main content

Table 1 Pipeline comparison

From: Illuminating the dark side of the human transcriptome with long read transcript sequencing

Match type

Polish

Lordec

TAMA low

TAMA high

Total Genes

25,731

166,766

168,328

38,743

Total Transcripts

126,288

753,756

752,996

135,218

Ensembl Loci Overlap

19,348

30,835

30,947

21,284

Ensembl Transcript Matches

17,948

24,660

24,691

15,854

Predicted Novel Gene Loci

8519

139,769

141,097

23,302

Predicted Novel Transcripts

106,243

724,316

723,759

118,148

  1. Comparison of gene and transcript numbers across pipelines broken down into different categories. Ensembl loci overlap refers to the number of Ensembl v94 annotation gene models that are overlapped on the same strand by gene models from each Iso-Seq annotation. Transcript matches refer to Ensembl v94 transcript models with identical exon-intron structures as transcript models in each Iso-Seq annotation. The Ensembl v94 human annotation consists of 58,735 gene loci and 206,601 unique transcript models. In some cases, multiple Ensembl gene loci are overlapped by a single Iso-Seq gene locus leading to the differences between matching loci and predicted novel loci