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Table 1 Reference-based mapping methods overview - summary of the four reference-based mapping method categories compared in this study

From: Comparing reference-based RNA-Seq mapping methods for non-human primate data

Method

Reference

Method subcategory

Representative

Notes

category

  

method

 

Unspliced

Genome or

Burrows-Wheeler

Bowtie2*

Index reference sequence, Rapidly look up candidate mapping loci.

Aligners

Transcriptome

Transform Method

 

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

   

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.

  1. *Bowtie2 may be considered a hybrid BWT-Seed Method, as multiple substrings are taken from each read for the BWT lookup of candidate mapping loci, and the alignment at each candidate loci is extended.