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Table 1 RMSE values in differential expression measurements

From: Limitations of alignment-free tools in total RNA-seq quantification

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)

  1. 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