RNA-Seq results

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 main results of the RNA-Seq analysis are two expression tracks (one for gene-level and one for transcript-level expression) and a mapping track. In addition, the following optional results can be selected:

The sections below elaborate on the report and the fusion gene table, and the main results are explained in detail in Interpreting the RNA-Seq analysis result.

RNA-Seq report
An example of the result of the option Create report is shown in figure 27.10.

Image mrna_seq_report
Figure 27.10: Report of an RNA-Seq run.

The report contains the following information:

Note that the report can be exported in pdf or Excel format.

Gene fusion reporting
When using paired data, there is also an option to create an annotation track summarizing the evidence for gene fusions. An example is shown in figure 27.11.

Image mrna_seq_gene_fusion
Figure 27.11: An example of a gene fusion table.

Each row represents one gene where read pairs suggest it could be fused with another gene. This means that each fusion is represented by two rows.

The Minimum read count option in figure 27.9 is used to make sure that only combinations of genes supported by at least this number of read pairs are included. The default value is 5, which means that at least 5 pairs need to connect two genes in order to report it in the result.

The result table shows the following information for each row:

Note that the reporting of gene fusions is very simple and should be analyzed in much greater detail before any evidence of gene fusions can be verified. The table should be considered more of a pointer to genes to explore rather than evidence of gene fusions. Please note that you can include the fusion genes track in a track list together with the reads tracks to investigate the mapping patterns in greater detail:

        File | New | Track List (Image tracklist)