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 29.19.

Image mrna_seq_gene_fusion
Figure 29.19: 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 29.10 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 | Genome Browser View (Image trackset_16_n_p)