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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