Import Known Fusion Information Track
Import Known Fusion Information Track can import information about known fusions from a tab separated text file. It outputs an annotation track (
) that can be used with Annotate Fusions with Known Fusion Information.
The importer can be found here:
Import (
) | Import Known Fusion Information Track (
)
The following options can be configured (figure 5.6):
- File A tab separated text file with the known fusion information. The first row in the file is a header. Each subsequent row lists the information for a known fusion.
Information is extracted from the following columns in the file:
5prime_geneand3prime_gene(mandatory): the name of the 5'/3' gene.5prime_bpand3prime_bp(optional): the position of the 5'/3' breakpoint.The position can be exact (e.g., 1364892), or uncertain (e.g., 1364887-1364895).
5prime_chrand3prime_chr(optional): the chromosome of the 5'/3' gene.5prime_strandand3prime_strand(optional): the strand (+/-) of the 5'/3' gene.
Further columns are added as additional attributes.
- Gene track An annotation track () with the gene annotations. The 5' and 3' genes in the provided file are matched to this track by gene names, with support for synonyms. If chromosome and/or strand information is available in the file:
- For genes that match the track:
- If the chromosome in the file and track do not match, the fusion is not imported.
- If the strand in the file and track do not match, the strand from the track is used.
- If the breakpoint position is not available, the entire gene region is used.
- For genes that do not match the track:
- The fusion is imported with the chromosome/strand provided in the file.
- Fusions with genes without a breakpoint position are not imported.
- For genes that match the track:
Figure 5.6: The available options when importing known fusion information.