Output files

Output of the filtering step (Part II)

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resultTable.xlsx

Excel file with the following columns:

• cohort: Name of the cohort that the sample is associated with.
• sample: Name of sample.
• caller: Fusion caller which called this fusion event (AR = Arriba, FC = FusionCatcher).
• gene1: 5' partner gene.
• gene2: 3' partner gene.
• chr1: Chromosome of 5' partner.
• pos1: Breakpoint within the 5' partner gene.
• chr2: Chromosome of 3' partner.
• pos2: Breakpoint within the 3' partner gene.
• cov: Number of fusion supporting reads.
• label: Fusion name.
• known: Indicates whether this fusion event was recurrently reported by public databases (ChimerDB, Mitelman).
• reciprocal: Indicates whether there exist a reciprocal fusion gene which is more common.
• karyo: Indicates if fusion event has evidence by karyotype (if clinical table was provided).
• mol: Indicates if fusion event has evidence by FISH/PCR (if clinical table was provided).
• PS: Promiscuity Score.
• tpm_gene1: Expression of the 5' partner gene in transcripts per million.
• tpm_gene2: Expression of the 3' partner gene in transcripts per million.
• fusion_tpm: Expression of the fusion gene in transcripts per million.
• FTS: Fusion Transcript Score.
• ev_level: Evidence level.
• RS: Robustness Score.
• callerOverlap: Indicates whether this fusion event was found by both fusion callers.

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filterrun.RData

R Workspace that was generated during the filtering pipeline. Useful for debugging (debug_flag must be set to 1 in FP_filter.sh).

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barplot_excluded_fusions.png

Fraction of fusion events that have been excluded by the single filtering steps.
Example

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violinplot_fts.png

Distribution of Fusion Transcript Scores of called fusion events.
Example

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violinplot_ps.png

Distribution of Promiscuity Scores of called fusion events.
Example

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TPM-FTS_3D_plot.html

Distribution of Fusion Transcript Scores of called fusion events in relation to the expression of their partner genes packed into an interactive 3D plot.

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circosplot_cohort_known / circosplot_cohort_unknown

Overview of known/novel robust fusion gene candidates in a circular genome plot (circos). Blue lines indicate known fusion events. Red lines indicate recurrent while grey lines indicate non-recurrent novel fusion events. Thickness of lines indicates recurrence.
Example