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FusionVisualizer

Post-processing tool for fusion transcripts visualization.

The component takes as inputs:

Ensembl annotation file and Ensembl release number as parameter (for hg19 use Ensembl release 75).
Fusion list: a tab separeted file with 4 columns containg the gene Ensembl IDs involved in the fusions and relative breakpoint coordinates. The order of the columns and the column names can be wathever, but they must be passed as parameter to the component.
Reads: single/paired-end reads of the sample.

The component creates two virtual genome references:

virtual_ref1.fa: reference that has in each sequence line the entire sequences of the two genes involved in each fusion merged together.
virtual_ref2.fa: reference that has in each sequence line the sequence of the fused gene (only the parts of the genes retained in the fusion, merged together).

The reads are then aligned to these two virtual references using STAR aligner (https://github.com/alexdobin/STAR).

The component outputs:

Fasta files of the two virtual references created (virtual_ref1.fa, virtual_ref2.fa).
GTF and GFF annotation files for the two virtual references (annotation1.gff3, annotation1.gtf for virtual_ref1.fa and annotation2.gff3, annotation2.gtf for virtual_ref2.fa).
SAM and Sorted Bam files of the alignments (align1.sorted.bam, align2.sorted.bam). For each alignment only the primary aligmenent of the mapped reads are retained for visualization.

The output can be visualized loading these files in IGV browser (https://www.broadinstitute.org/igv/). In IGV browser: "Genomes->Load Genome from File..." and select either virtual_ref1.fa or virtual_ref2.fa; "File->Load from file..." and select respectively annotation1/2.gtf,annotation1/2.gff3, align1/2.sorted.bam.

Install ensembl api following instructions from http://www.ensembl.org/info/docs/api/api_git.html Also install bioperl-run https://github.com/bioperl/bioperl-run

Version	1.1
Bundle	sequencing
Categories	Alignment
Authors	Gabriele Partel (gabrielepartel@gmail.com)
Issue tracker	View/Report issues
Requires	BioPerl ; Ensembl Perl API ; STAR ; Samtools ; installer (bash)
Source files	component.xml fusionvisualizercomp.sh
Usage	Example with default values FusionVisualizer( fusionList = CSV, annotations = GTF, reads = FASTQ, //mates = FASTQ, as = "0.95", gene3pBP = "gene3p_bp", gene3pID = "gene3p_id", gene5pBP = "gene5p_bp", gene5pID = "gene5p_id", release = "84", threads = "8" )

Inputs

Name	Type	Mandatory	Description
fusionList	CSV	Mandatory	4 columns tab separated file containing a header line with the column names and a line for each fusion annotated with the IDs of the genes involved and the fusion breakpoints in 1-based coordinates. The column names must be passed as parameters.
annotations	GTF	Mandatory	Ensembl gtf annotation file.
reads	FASTQ	Mandatory	Single-end or first paired-end (reads) file. (The file format allowed are: .fa,.fq,.fq.gz).
mates	FASTQ	Optional	Second paired-end (mates) files (leave empty if single-end). (The file format allowed are: .fa,.fq,.fq.gz).

Outputs

Name	Type	Description
folder	BinaryFolder	Output folder containing the output files

Parameters

Name	Type	Default	Description
as	string	"0.95"	STAR --outFilterScoreMinOverLread parameter: Alignment will be output if its score is higher than or equal to this value (normalized to the read length).
gene3pBP	string	"gene3p_bp"	3'pair gene breakpoint coordinate column name in fusionList.
gene3pID	string	"gene3p_id"	3'pair gene ID column name in fusionList.
gene5pBP	string	"gene5p_bp"	5'pair gene breakpoint coordinate column name in fusionList.
gene5pID	string	"gene5p_id"	5'pair gene ID column name in fusionList.
release	string	"84"	Ensembl release number.
threads	string	"8"	STAR -runThreadN parameter: number of threads used by STAR.

Test cases

Test case	Parameters▼	IN fusionList	IN annotations	IN reads	IN mates	OUT folder
case1	(missing)	fusionList	annotations	reads	mates	(missing)

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