Fig. 2

Read mapping and transcript identification strategies. Three basic strategies for regular RNA-seq analysis. a An annotated genome is available and reads are mapped to the genome with a gapped mapper. Next (novel) transcript discovery and quantification can proceed with or without an annotation file. Novel transcripts are then functionally annotated. b If no novel transcript discovery is needed, reads can be mapped to the reference transcriptome using an ungapped aligner. Transcript identification and quantification can occur simultaneously. c When no genome is available, reads need to be assembled first into contigs or transcripts. For quantification, reads are mapped back to the novel reference transcriptome and further analysis proceeds as in (b) followed by the functional annotation of the novel transcripts as in (a). Representative software that can be used at each analysis step are indicated in bold text. Abbreviations: GFF General Feature Format, GTF gene transfer format, RSEM RNA-Seq by Expectation Maximization