Table 5 Precision of assembled transcripts for human brain 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 | 42.7 | 63.0 | 41.8 | 48.9 | 27.9 | 28.9 | 40.6 | 60.1 | 38.9 |
Exon | 76.5 | 92.3 | 79.0 | 79.4 | 73.1 | 73.4 | 72.9 | 90.2 | 76.0 |
Intron | 88.0 | 96.9 | 92.3 | 88.7 | 91.7 | 91.1 | 82.9 | 94.6 | 88.2 |
Intron Chain | 79.1 | 94.5 | 85.9 | 80.1 | 84.4 | 83.3 | 72.1 | 90.7 | 79.6 |
Transcript | 57.5 | 83.0 | 60.2 | 62.1 | 51.0 | 51.6 | 54.8 | 80.9 | 57.8 |
Locus | 32.2 | 61.5 | 32.4 | 37.2 | 24.1 | 24.9 | 30.5 | 58.9 | 31.2 |