During a previous section of this tutorial, a spreadsheet named unexplained_regions was generated. This spreadsheet contains locations where reads map to the genome but are not annotated by the transcript database, in this case, RefSeqGene. Theunexplained_regions spreadsheet is potentially very interesting as it may contain novel findings.

• Right click column 6. Average Coverage and select Sort Descending from the menu
• Select Find Overlapping Genes from the Tools option in the command toolbar (Figure 1)
  
  

Figure 1. Selecting Find Overlapping Genes from Tools in the command toolbar

• Select Add a new column with the gene nearest to the region in the Find Overlapping Genes dialog (Figure 2)
• Select OK

Figure 2. Find Overlapping Genes

• Select RefSeqTranscripts – 2014-01-03 from the Output Overlapping Features dialog (Figure 3)

Please note that it is recommended that you annotate with the same database as when you performed mRNA quantification.

• Select OK

Figure 3. Select the database to search for overlapping features

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