From: Comparing reference-based RNA-Seq mapping methods for non-human primate data
Method | Reference | Method subcategory | Representative | Notes |
---|---|---|---|---|
category | Â | Â | method | Â |
Unspliced | Genome or | Burrows-Wheeler | Bowtie2* | Index reference sequence, Rapidly look up candidate mapping loci. |
Aligners | Transcriptome | Transform Method | Â | Typically faster and less sensitive than Seed Methods. |
 |  | Seed Method | Stampy | Align short subsequences of reads to find candidate mapping loci, |
 |  |  |  | Narrow candidates by extending alignments. Typically slower and |
 |  |  |  | more sensitive than Burrows-Wheeler Transform Methods. |
Spliced | Genome | Exon First Method | TopHat2 | Align whole reads with Unspliced Aligners, Search for spliced |
Aligners | Â | Â | Â | alignments in remaining reads. Typically faster and less sensitive |
 |  |  |  | than Seed and Extend Methods. |
 |  | Seed and Extend Method | GSNAP | Align short subsequences of reads to find candidate mapping loci, |
 |  |  |  | Narrow candidates by extending alignments. Typically slower and |
 |  |  |  | more sensitive than Exon First Methods. |