Specifying reads and reference

To start the RNA-Seq analysis, go to:

        Toolbox | Transcriptomics Analysis (Image expressionfolder) | 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 26.4.

Image mrna_seq_step2-biomedical
Figure 26.4: 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 the reference content to map to. Note that this is only relevant when using an annotated reference:

Note: If the options "One reference sequence per transcript" or "Also map to inter-genic regions" are chosen, the internal data structure used for mapping the reads can be reused, resulting in a dramatically reduced runtime. For more information about this, please see Reference caching.


... values26.1
The reads will indirectly impact the RPKM expression values as they will be counted in the total number of mapped reads which is used to calculate RPKM (Definition of RPKM)