RNA-Seq output options

Clicking Next will allow you to specify the output options as shown in figure 27.9.

Image mrna_seq_step4
Figure 27.9: Selecting the output of the RNA-Seq analysis.

The Output options are:

The standard output for the RNA-Seq analysis is a table showing values for each gene. From the table, mappings can be opened individually by clicking on the button labeled Open mapping found at the bottom of the table or by double clicking on one of the entries in the table (see 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 under Expression value:

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.