Table 1. Performance of TopHat2 and STAR spliced aligners on Total mRNA-seq and DMD mRNA-seq data for the detection of exon junctions in the DMD transcript.
| TopHat2 |
STAR |
|||
|---|---|---|---|---|
| Total mRNA-seq | DMD mRNA-seq | Total mRNA-seq | DMD mRNA-seq | |
| exon junctions: all | 78 | 93 | 98 | 128 |
| exon junctions: canonical | 73 | 78 | 78 | 78 |
| canonical junctions mean coverage (+/−SD) | 142 (+/−84) | 697 (+/−134) | 117 (+/−69) | 1144 (+/−254) |
| PE1a junctions mean coverage | 0 | 5 | 0 | 97 |
“Exon junctions: all” refers to the number of detected junctions in the RNA-seq datasets including both canonical (n = 78 in the DMD gene) and new junctions due to alternative splicing events. Mean coverages given by TopHat2 and STAR for canonical junctions and for pseudoexon 1a (PE1a), a well-documented example of pseudoexon insertion in the mature muscular DMD transcript, are indicated.