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Table 4 Analysis of real single-end data

From: Adaptable probabilistic mapping of short reads using position specific scoring matrices

  

Unfiltered

Filtered

 
 

Mapper

Aligned

Aligned

Time (s)

  

(fraction)

(fraction)

 

a) Ancient DNA

 

BWA-PSSMA

0.01000

0.00763

60.75

 

BWA-PSSM

0.01000

0.00759

51.61

 

BWA

0.00906

0.00708

18.63

 

BWA-MEM

0.01629

0.01177

21.24

 

Bowtie

0.00892

*

63.78

 

Bowtie2

0.01087

0.00691

16.48

 

GEM

0.06106

*

18.69

b) Real PAR-CLIP

 

BWA-PSSMPC

0.600

0.148

146.08

 

BWA-PSSM

0.476

0.114

141.08

 

BWA

0.483

0.140

166.99

 

BWA-MEM

0.198

0.022

236.51

 

Bowtie

0.463

*

84.81

 

Bowtie2

0.453

0.076

43.11

 

GEM

0.227

0.227

280.57

  1. Comparison of run times and fraction of reads mapped for the four mappers on two real data sets, each containing 100,000 Illumina reads. a) Reads of ancient DNA mapped to the horse genome. The run times do not include the time required to build the PSSMs. b) Reads of PAR-CLIP data mapped to the human genome. BWA-PSSM only makes use of the error model given by equation (1), while BWA-PSSMA also uses the ancient DNA damage model and BWA-PSSMPC also uses the T-to-C transition model characterizing PAR-CLIP data. The symbol ’*’ indicates that the mapper does not provide MapQ scores.