Table 6 Precision of assembled transcripts for mouse embryonic stem cell single cell dataset across different transcript assembly approaches
From: Cloud accelerated alignment and assembly of full-length single-cell RNA-seq data using Falco
Feature | STAR + StringTie (with reference) | STAR + Scallop | HISAT + StringTie | ||||||
|---|---|---|---|---|---|---|---|---|---|
Falco alignment + individual assembly (%) | Falco alignment + pooled assembly (%) | Falco transcript assembly mode (%) | Falco alignment + individual assembly (%) | Falco alignment + pooled assembly (%) | Falco transcript assembly mode (%) | Falco alignment + individual assembly (%) | Falco alignment + pooled assembly (%) | Falco transcript assembly mode (%) | |
Base | 52.8 | 90.3 | 55.0 | 56.2 | 34.5 | 38.4 | 51.1 | 88.0 | 51.0 |
Exon | 69.8 | 95.9 | 78.3 | 74.6 | 71.7 | 73.1 | 69.1 | 95.3 | 76.2 |
Intron | 77.0 | 96.9 | 88.0 | 80.9 | 87.1 | 85.6 | 76.0 | 96.4 | 86.3 |
Intron Chain | 57.0 | 93.4 | 76.1 | 62.9 | 73.0 | 70.5 | 56.4 | 92.3 | 73.1 |
Transcript | 48.1 | 90.9 | 58.8 | 54.8 | 47.8 | 50.8 | 48.5 | 90.2 | 56.2 |
Locus | 40.4 | 86.1 | 41.7 | 46.3 | 30.1 | 33.9 | 40.1 | 85.8 | 39.5 |