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 | |
 |  | 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 | |
 |  | Exon junction libraries | |
Normalization | Library size | Â | For example, [34] |
 | RPKM | ERANGE | [32] |
 | TMM | edgeR | [48] |
 | Upper quartile | Myrna | |
Differential expression | Poisson GLM | DEGseq | [100] |
 |  | Myrna | [47] |
 | Negative binomial | edgeR | [57] |
 |  | DESeq | [46] |
 |  | baySeq | [58] |
Systems biology | Gene Ontology analysis | GOseq | [68] |