Figure 9

Analysis protocol. (A) The mapping result for a sequence read that is gene model dependent, where none of the gene models are complete; (B) “two-stage” mapping protocol: at Stage #1, all RNA-Seq reads are mapped to a reference transcriptome only, and then only the mapped reads are saved into a new FASTQ file; at Stage #2, those remaining reads are mapped to the genome with and without the use of a gene model in the mapping step; (C) The protocol for classifying uniquely mapped sequence reads into four categories, i.e., “Identical”, “Alternative”, “Multiple” and “Unmapped” (or Fail).