Table 1.
RMSE values in differential expression measurements
| RNA type | HISAT2+featureCounts | TGIRT-map | Kallisto | Salmon |
|---|---|---|---|---|
| Antisense | 0.455 | 0.452 | 0.476 | 0.442 |
| (5380) | (5361) | (4855) | (5261) | |
| ERCC | 0.406 | 0.399 | 0.342 | 0.336 |
| (88) | (87) | (88) | (88) | |
| miRNA | 0.589 | 0.547 | 0.575 | 0.552 |
| (558) | (1289) | (952) | (1108) | |
| Mt | 0.21 | 0.137 | 0.173 | 0.235 |
| (36) | (34) | (36) | (36) | |
| Other ncRNA | 0.461 | 0.461 | 0.501 | 0.5 |
| (20611) | (20822) | (18573) | (21614) | |
| Other sncRNA | 0.511 | 0.483 | 0.514 | 0.501 |
| (2236) | (3025) | (2560) | (3077) | |
| Protein coding | 0.229 | 0.231 | 0.302 | 0.287 |
| (19944) | (19965) | (19712) | (19865) | |
| rRNA | 0.733 | 0.608 | 0.582 | 0.186 |
| (4) | (4) | (4) | (4) | |
| snoRNA | 0.383 | 0.395 | 0.429 | 0.438 |
| (620) | (704) | (623) | (742) | |
| tRNA | 0.23 | 0.2 | 0.478 | 0.468 |
| (55) | (58) | (48) | (48) | |
| vaultRNA | 0.171 | 0.258 | 0.417 | 0.405 |
| (6) | (8) | (8) | (9) |
Numbers of genes tested by DESeq2 are shown in parentheses. RNA-type annotations were generated from Ensembl [30]. “Other ncRNA” represents the following RNA types: sense intronic, 3prime overlapping ncRNA, processed transcript, sense overlapping, lincRNA, and all pseudogenes. “Other sncRNA” represents the following RNA types: misc RNA, snRNA, scaRNA, sRNA, scRNA. Mt represents all mitochondrial genes, including mitochondrial-encoded tRNAs. vaultRNA represents any Ensembl gene names with Vault or VTRNA