Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq

BMC Bioinformatics

Table 1 Analysis tools used in this study

Read aligner	RA code	Expression modeler	EM code	Differential expression	DE code
Bowtie2	Bw	BitSeq	Bs	Ballgown	Bl
HISAT2	Hs	cufflinks	Cu	BitSeq	Bs
Kallisto	Ka	htseq	Ht	baySeq	By
Salmon-FMD	Sf	IsoEM	Ie	cuffdiff	Cd
Sailfish	Sl	kallisto	Ka	DESeq2	De
SeqMap	Sm	RSEM	Rm	EBseq	Eb
Salmon-Quasi	Sq	rSeq	Rs	edgeR	Er
STAR	Sr	Sailfish	Sl	limma + voom	Lo
TopHat2	Th	Salmon	Sn	limma + vst	Lv
		STAR	Sr	NBPseq	Nb
		Stringtie	St	NOISeqBIO	No
		eXpress	Xs	SAMseq	Sa
				Sleuth	Su

Abbreviations specified in the table are used throughout the figures. Additional details are available in Additional file 1

ISSN: 1471-2105