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Table 1 The five mapper and database combinations used by StrongArm

From: The landscape of coding RNA editing events in pediatric cancer

Priority Mapper Database
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.