Gene fusion reporting

When using paired data, there is also an option to create a table summarizing the evidence for gene fusions. An example is shown in figure 27.10.

Image mrna_seq_gene_fusion
Figure 27.10: An example of a gene fusion table.

The table includes one row for each broken read pair where the reads are placed in different genes. The Minimum read count option 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 broken pairs need to connect two genes, in order to include the broken pairs for this gene combination in the result table.

The result table shows the following information for each read:

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 extract the reads as a separate sequence list for further investigation.