Table 1 Differential expression analysis comparing gene vs. transcript models using simulated data
From: Best practices on the differential expression analysis of multi-species RNA-seq
Quantification method | DESeq2 DE genes detected | DESeq2 DE transcripts detected | DESeq2 false positive DE genes | DESeq2 false positive DE transcripts | edgeR DE genes detected | edgeR DE transcripts detected | edgeR false positive DE genes | edgeR false positive DE transcripts |
|---|---|---|---|---|---|---|---|---|
FADU | 684 (54.9%) | 440 (79.1%) | 7 (0.56%) | 11 (2.0%) | 947 (76.0%) | 439 (79.0%) | 34 (2.7%) | 12 (2.2%) |
FADU -em_iterations 10 | 686 (55.1%) | 438 (78.8%) | 10 (0.8%) | 12 (2.2%) | 955 (76.7%) | 436 (78.4%) | 37 (3.0%) | 12 (2.2%) |
FADU -remove_multimapped | 702 (56.3%) | 435 (78.2%) | 4 (0.32%) | 5 (0.9%) | 974 (78.2%) | 447 (80.4%) | 32 (2.6%) | 9 (1.6%) |
featureCounts | 694 (55.7%) | 434 (78.1%) | 5 (0.4%) | 5 (0.9%) | 936 (75.1%) | 441 (79.3%) | 24 (1.9%) | 10 (1.8%) |
featureCounts -O | 775 (62.2%) | 515 (92.6%) | 18 (1.44%) | 54 (9.7%) | 1008 (80.9%) | 522 (93.9%) | 43 (3.5%) | 61 (11.0%) |
featureCounts -O -fraction | 734 (58.9%) | 505 (90.8%) | 14 (1.12%) | 20 (3.6%) | 1000 (80.3%) | 528 (95.0%) | 47 (3.8%) | 44 (7.9%) |
HTSeq -m union | 644 (51.7%) | 428 (77.0%) | 4 (0.32%) | 5 (0.9%) | 909 (73.0%) | 436 (78.4%) | 40 (3.2%) | 12 (2.2%) |
HTSeq -m intersection-strict | 607 (48.7%) | 436 (78.4%) | 1 (0.08%) | 5 (0.9%) | 803 (64.5%) | 442 (79.5%) | 24 (1.9%) | 14 (2.5%) |
HTSeq -m intersection-nonempty | 656 (52.7%) | 436 (78.4%) | 3 (0.24%) | 5 (0.9%) | 903 (72.5%) | 442 (79.5%) | 31 (2.5%) | 14 (2.5%) |
HTSeq -m union -nonunique all | 769 (61.7%) | 509 (91.6%) | 18 (1.44%) | 48 (8.6%) | 1005 (80.7%) | 519 (93.4%) | 47 (3.8%) | 65 (11.7%) |
kallisto | 675 (54.2%) | 526 (94.6%) | 9 (0.72%) | 11 (2.0%) | 946 (75.9%) | 532 (95.7%) | 41 (3.3%) | 22 (4.0%) |
Salmon -validateMappings | 676 (54.3%) | 525 (94.4%) | 4 (0.32%) | 8 (1.4%) | 946 (75.9%) | 534 (96.0%) | 44 (3.5%) | 25 (4.5%) |
Salmon -validateMappings -allowDovetail | 675 (54.2%) | 525 (94.4%) | 4 (0.32%) | 9 (1.6%) | 946 (75.9%) | 534 (96.0%) | 46 (3.7%) | 23 (4.1%) |