How is gene model used in RNA-Seq alignment

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The mapping strategy is:

  1. Map all reads to the transcriptome
  2. Map (unmapped reads + reads mapped to transcriptome with mismatches) to genome searching novel exon junctions
  3. Compare the mapping score between genome and transcriptome mapping; choose the best mapping and choose transcriptome mapping locations if it is a tie
  4. Translate all transcriptome mapping locations to genomic coordinates to count the final # of mapping locations
  5. Merge alignments from two stages

unmapped reads are ones cannot be mapped less than specified penalty. If you are using auto penalty, it is described in AutoPenalty.