Where does the html file come from?

[alexjfortuna]

From Fusion inspector I have the following files, and I would like to generate a fusion report:

chckpts_dir/
cytoBand.txt finspector.gtf finspector.bed finspector.igv.FusionJuncSpan finspector.bed.sorted.bed.gz finspector.junction_reads.bam finspector.bed.sorted.bed.gz.tbi finspector.junction_reads.bam.bai finspector.consolidated.cSorted.bam finspector.junction_reads.bam.bed finspector.consolidated.cSorted.bam.bai finspector.junction_reads.bam.bed.sorted.bed.gz finspector.fa finspector.junction_reads.bam.bed.sorted.bed.gz.tbi finspector.fa.fai finspector.spanning_reads.bam finspector.fusion_inspector_web.json finspector.spanning_reads.bam.bai finspector.fusion_predictions.final.abridged finspector.spanning_reads.bam.bed finspector.fusion_predictions.final.abridged.FFPM finspector.spanning_reads.bam.bed.sorted.bed.gz finspector.fusion_predictions.final.abridged.FFPM.annotated finspector.spanning_reads.bam.bed.sorted.bed.gz.tbi finspector.fusion_predictions.final.abridged.FFPM.annotated.coding_effect

I seem to have just about every file type except for html. I am likely misinterpreting what I am supposed to do. Any tips would be appreciated. Thank you!

[brianjohnhaas]

Hi,

If you're using the current production version, then you would use the stand-alone desktop igv viewer as shown: https://github.com/FusionInspector/FusionInspector/wiki

IGV-js support in the non-galaxy-based deployment will be fully supported in the next FI release, early next year.

hope this helps,

~b

On Thu, Nov 29, 2018 at 3:09 PM alexjfortuna notifications@github.com wrote:

From Fusion inspector I have the following files, and I would like to generate a fusion report:

chckpts_dir/ cytoBand.txt finspector.gtf finspector.bed finspector.igv.FusionJuncSpan finspector.bed.sorted.bed.gz finspector.junction_reads.bam finspector.bed.sorted.bed.gz.tbi finspector.junction_reads.bam.bai finspector.consolidated.cSorted.bam finspector.junction_reads.bam.bed finspector.consolidated.cSorted.bam.bai finspector.junction_reads.bam.bed.sorted.bed.gz finspector.fa finspector.junction_reads.bam.bed.sorted.bed.gz.tbi finspector.fa.fai finspector.spanning_reads.bam finspector.fusion_inspector_web.json finspector.spanning_reads.bam.bai finspector.fusion_predictions.final.abridged finspector.spanning_reads.bam.bed finspector.fusion_predictions.final.abridged.FFPM finspector.spanning_reads.bam.bed.sorted.bed.gz finspector.fusion_predictions.final.abridged.FFPM.annotated finspector.spanning_reads.bam.bed.sorted.bed.gz.tbi finspector.fusion_predictions.final.abridged.FFPM.annotated.coding_effect

I seem to have just about every file type except for html. I am likely misinterpreting what I am supposed to do. Any tips would be appreciated. Thank you!

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[jrobinso]

@alexjfortuna as Brian indicates this is a pre-release non supported project at present. However, if you want to give it a try you can try the html file at example/FI_viewer/igvjs_fusion.html. There are references to the other files you mention in the html file itself, which should be considered a template. Its simplest to put it in the same directory as the other files. Then run as indicated in the readme

python create_fusion_report.py example/FI_viewer/igvjs_fusion.html

For emphasis -- this is a pre-release development project and details could change at any time. For real work use the supported method indicated by Brian for now.