Specifying reads and reference

To start the RNA-Seq analysis, go to:

        Toolbox | RNA-Seq Analysis (Image rna_seq_group_closed_16_n_p) | RNA-Seq Analysis (Image rnaseq)

This opens a dialog where you select the sequencing reads. Note that you need to import the sequencing data into the Workbench before it can be used for analysis. Importing read data is described in Import Sequencing Data.

If you have several samples that you wish to analyze independently and compare afterwards, you can run the analysis in batch mode.

Click Next when the sequencing data are listed in the right-hand side of the dialog.

You are now presented with the dialog shown in figure 29.3.

Image mrna_seq_step2-biomedical
Figure 29.3: Defining a reference genome for RNA-Seq.

At the top, there are three options concerning how the reference sequences are annotated.

At the bottom of the dialog you can choose between these two options:

If spike-ins have been used, the quality control results are shown in the output report. So when using spike-in, make sure that the option to output a report is checked.

To learn how to import spike-in control files, see Import RNA Spike-in.