Table 1 The five mapper and database combinations used by StrongArm

1

BWA

RefSeq: Every RefSeq transcript found in UCSC’s refFlat table [38]; useful for finding canonical splicing.

2

BWA

RefSeq alternate exons: Fragments of RefSeq transcripts formed by choosing an ordered subset of exons from each gene that contains a single pair of adjacent exons which are not adjacent in any annotation, and with 100 bp of sequence on either side of the event; useful for finding alternate splicing.

3

BWA

AceView: Every AceView transcript found in UCSC’s assembly table; useful for various other known splice forms.

4

BWA

Whole genome: the genome reference sequence (no translation is performed); useful for unspliced reads and some structural variation events.

5

STAR

Whole genome (STAR): the genome reference sequence (no translation is performed); useful for some novel exons and structural variation events.