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 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.

Please note that the main effect of the choice of Expression value type at this stage is that it determines the values types that will be exported if you choose to export tables of values to text or excel format files. In other words: if you wish to export transcript values later, then choose transcript values at this stage. For other purposes, such as Interpreting the RNA-Seq analysis result, or for carrying out downstream expression analysis, you can choose later between the different output types available.

You can also choose to create a sequence list of the non-mapped sequences. 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.