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Table 1 Software methods and tools for differential expression analysis of RNA-seq

From: From RNA-seq reads to differential expression results

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