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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%)