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

BMC Genomics

Table 1 Pipeline comparison

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

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

ISSN: 1471-2164