RNA-Seq output options
Clicking Next will allow you to specify the output options as shown in figure 27.9.
Figure 27.9: Selecting the output of the RNA-Seq analysis.
The standard output is a table showing values for each gene and the option to open the mapping (see more Interpreting the RNA-Seq analysis result). For eukaryotes, the expression of individual transcripts is also reported. The expression measure for use in further analysis can be specified at this point as well. By default, this is set to Genes RPKM.
The value chosen for measuring expression is used for Interpreting the RNA-Seq analysis result, and for carrying out downstream expression analysis. You can change this to a different value at a later point by opening the result and set the Expression value at the bottom of the table.
Under output options it is also possible to create a sequence list of the un-mapped sequences (marked with a red arrow in figure 27.9). This list could be used to do de novo assembly and perform BLAST searches to see if you can identify new genes or otherwise further investigate the results.
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