Table 1

Software methods and tools for differential expression analysis of RNA-seq

Analysis step

Method

Implementation

References


Mapping

General aligner

GMAP/GSNAP

[91]

BFAST

[20]

BOWTIE

[25]

CloudBurst

[92]

GNUmap

[93]

MAQ/BWA

[23]

PerM

[19]

RazerS

[94]

Mrfast/mrsfast

[22]

SOAP/SOAP2

[24,95]

SHRiMP

[21]

De novo annotator

QPALMA/GenomeMapper/PALMapper

[37]

SpliceMap

[96]

SOAPals

[95]

G-Mo.R-Se

[97]

TopHat

[40]

SplitSeek

[36]

De novo transcript assembler

Oases

[98]

MIRA

[99]

Summarization

Isoform-based

Cufflinks

[11]

ALEXA-seq

[10]

Gene-based

Count exons only

For example, [34,45]

Exon junction libraries

[34,44]

Normalization

Library size

For example, [34]

RPKM

ERANGE

[32]

TMM

edgeR

[48]

Upper quartile

Myrna

[45,47]

Differential expression

Poisson GLM

DEGseq

[100]

Myrna

[47]

Negative binomial

edgeR

[57]

DESeq

[46]

baySeq

[58]

Systems biology

Gene Ontology analysis

GOseq

[68]


Abbreviations: GLM, generalized linear model; RPKM, reads per kilobase of exon model per million mapped reads; TMM, trimmed mean of M-values.

Oshlack et al. Genome Biology 2010 11:220   doi:10.1186/gb-2010-11-12-220