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RNAseq-fusion-nf

Fusion-genes discovery from RNAseq data using STAR-Fusion

CircleCI Docker Hub

Workflow representation

Description

Performs Fusion-gene discovery from junction reads identified by STAR during alignment. See citation of STAR-Fusion below.

Dependencies

  1. Nextflow : for common installation procedures see the IARC-nf repository.
  2. STAR-Fusion

In addition, STAR-Fusion requires a CTAT bundle with reference genome and annotations.

A conda receipe, and docker and singularity containers are available with all the tools needed to run the pipeline (see "Usage")

Input

Type Description
input_folder Folder containing fastq files and STAR junction files

Specify the test files location

Parameters

  • Mandatory

Name Example value Description
--CTAT_folder . Folder with STAR-Fusion bundle (CTAT)

  • Optional

Name Default value Description
--input_file NULL Input file (comma-separated) with 4 columns: SM(sample name), pair1 (path to fastq pair 1), pair2 (path to fastq pair 2), and junction (path to junction file)
--output_folder results_fusion Output folder
--fastq_ext fq.gz Extension of fastq files
--suffix1 _1 Suffix of 1st element of fastq files pair
--suffix2 _2 Suffix of 2nd element of fastq files pair
--junction_suffix Chimeric.SJ.out.junction Suffix of STAR chimeric junction files
--starfusion_path /usr/local/src/STAR-Fusion/STAR-Fusion Path to STAR-fusion executable; note that the default is set to the location in the singularity container
--cpu 2 Number of cpu used by bwa mem and sambamba
--mem 2 Size of memory used for mapping (in GB)

Note: using the input_file mode allows to specify multiple fastq files for a given sample, that are merged during the alignment phase.

  • Flags

Flags are special parameters without value.

Name Description
--junctions Option to use STAR junction files already generated
--help Display help

Note: when the --junctions option is not used, the junction column of the input file is ignored.

Usage

nextflow run iarcbioinfo/RNAseq-fusion-nf -r v1.1 -profile singularity  --input_folder input --CTAT_folder CTAT --output_folder output

To run the pipeline without singularity just remove "-profile singularity"; you can also directly download a singularity image at https://data.broadinstitute.org/Trinity/CTAT_SINGULARITY/STAR-Fusion/ using the command singularity pull https://data.broadinstitute.org/Trinity/CTAT_SINGULARITY/STAR-Fusion/star-fusion.v1.9.0.simg. Alternatively, one can run the pipeline using a docker container (-profile docker) the conda receipe containing all required dependencies (-profile conda).

Output

Type Description
output Folder with fusion genes file

Directed Acyclic Graph

DAG

Contributions

Name Email Description
Nicolas Alcala [email protected] Developer to contact for support

References

Haas, B. J., Dobin, A., Li, B., Stransky, N., Pochet, N., & Regev, A. (2019). Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods. Genome biology, 20(1), 213.