Terra

Run STAR-Fusion on Terra - see the STAR-Fusion Terra featured workspace.

1. Upload your FASTQ files to your workspace bucket.

   Example:

   gsutil -m cp /foo/bar/projects/*.fastq.gz gs://your_workspace_bucket_name
   

   The workspace bucket gs url is listed on the workspace dashboard.

   Please see here for additional documentation.

2. Clone the workflow to your own workspace.

   See the Terra documentation for adding a workflow.

3. In your workspace, open star_fusion_workflow in the WORKFLOWS tab. If you are running a single sample, select Run workflow with inputs defined by file paths, otherwise select Run workflow(s) with inputs defined by data table. Terra uses a workspace data table to run a workflow over multiple samples. Enter the workflow parameters and and click the Save button.

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Inputs

Please see the description of important inputs below.

Column	Description
left_fq	FASTQ file for read1
right_fq	FASTQ file for read2
genome	An acronym (either grch38_gencode_v32_1.8 or mouse_gencode_m23_1.8), or a gs:// URL to a custom tar.gz2 genome bundle archive.
chimeric_out_junction	In lieu of FASTQ files, provide previous STAR output. For kickstart mode
sample_id	Sample id
fusion_inspector	inspect or validate. Runs FusionInspector in either 'inspect' or 'validate' mode
additional_flags	e.g --no_annotation_filter --min_FFPM 0

Outputs

Column	Description
bam	Aligned BAM
star_log_final	STAR aligner log file.
junction	Chimeric alignments
sj	High confidence collapsed splice junctions in tab-delimited format
fusion_predictions	Tab-delimited file containing predicted fusions.
fusion_predictions_abridged	Same as fusion_predictions file but excludes the identification of the evidence fusion reads
fusion_inspector_inspect_web	Interactive html report from FusionInspector inspect
fusion_inspector_inspect_fusions_abridged	Abridged output from FusionInspector inspect
fusion_inspector_validate_web	Interactive html report from FusionInspector validate
fusion_inspector_validate_fusions_abridged	Abridged output from FusionInspector validate
extract_fusion_reads	Optional FASTQ output if --extract_fusion_reads is provided as part of additional_flags input

Please see here for a detailed description of STAR-Fusion outputs and here, for a detailed description of FusionInspector outputs.