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1. Unspliced mapping: BWA. We used BWA to map reads from two conditions C1 and C2 to our genometranscriptome.
- Unspliced mappers are typically faster (particularly those using BWT).
- Unspliced mappers will miss/misalign reads that span exon-exon junctions.
- Unspliced mappers are best when mapping RNA-Seq data directly to the transcriptome.
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