EricScript Output

EricScript output.

The /PATH/TO/OUTPUT/ folder contains the results of the analysis. Predicted gene fusion products are reported in 2 files:

• samplename.results.total.csv: contains all the predicted gene fusions.

• samplename.results.filtered.csv: contains the predicted gene fusions with W.EricScore > 0.63 (see the paper).

For each predicted gene fusion product, EricScript outputs several important information including the names of 5’and 3’ genes and their corresponding biological descriptions, the genomic breakpoint positions for both the genes, the sequence that arises from the fusion process and the type of fusion (inter-chromosomal, intra-chromosomal, read through or CIS). Moreover, we report a raw estimation of gene expression of each of the two fused genes and of the gene fusion product and the five probability scores (GJS, ES, US, EricScore and W.EricScore). Read the paper for more details.

Field Name	Content
GeneName1	official gene name of 5' gene.
GeneName2	official gene name of 3' gene.
chr1	chromosome of 5' gene.
GenomicBreakpoint1	predicted genomic breakpoint on 5' gene.
strand1	strand (-/+) of 5' gene.
chr2	chromosome of 3' gene.
GenomicBreakpoint2	predicted genomic breakpoint on 3' gene.
strand2	strand (-/+) of 3' gene.
EnsemblGene1	Ensembl gene ID of 5' gene.
EnsemblGene2	Ensembl gene ID of 3' gene.
crossingreads	the number of paired end discordant reads.
spanningreads	the number of paired end reads spanning the junction.
mean.insertsize	mean of insert sizes of crossing + spanning reads.
homology	if filled, all the homologies between the fusion junction and Ensembl genes.
fusiontype	intra-chromosomal, inter-chromosomal, read-through or CIS.
InfoGene1	gene information about 5' gene.
InfoGene2	gene information about 3' gene.
JunctionSequence	predicted junction fusion sequence.
GeneExpr1	Read count based estimation of the expression level of 5' gene.
GeneExpr2	Read count based estimation of the expression level of 3' gene.
GeneExpr_fused	Read count based estimation of the expression level of the predicted chimeric transcript.
ES	Edge probability score.
GJS	Genuine Junction probability score.
US	Uniqueness probability score.
EricScore	EricScore probability score.
W.EricScore	W.EricScore probability score.