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Update README
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jpfeil committed Aug 30, 2017
1 parent e636f90 commit 548277e
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15 changes: 8 additions & 7 deletions README.md
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Expand Up @@ -13,7 +13,7 @@ Gene fusions play a major role in tumorigenesis, so it is crucial that Treehouse

REPOSITORY: ucsctreehouse/fusion

TAG: 0.1.0
TAG: 0.2.0


##### Input files
Expand All @@ -30,12 +30,14 @@ optional arguments:
--output-dir OUTPUT_DIR
Output directory
--genome-lib-dir GENOME_LIB_DIR
Reference genome directory
Reference genome directory (can be tarfile)
--CPU CPU Number of jobs to run in parallel
--genelist GENELIST
--skip-filter Skips gene-list filter
-F, --run-fusion-inspector
Runs FusionInspector on STAR-Fusion output
--star-fusion-results STAR_FUSION_RESULTS
Skips STAR-Fusion and runs FusionInspector
--save-intermediates Does not delete intermediate files
--root-ownership Does not change file ownership to user
--test Runs the pipeline with dummy files
Expand All @@ -57,20 +59,19 @@ docker run -it --rm -v `pwd`:/data ucsctreehouse/fusion:0.1.0 \
STAR-Fusion Output
* STAR-Fusion candidates and fusion fragments per million mapped read values
* star-fusion-non-filtered.final
* star-fusion-non-filtered.final.bedpe
* Fusions where donor and acceptor genes passed the gene-list filter
* star-fusion-gene-list-filtered.final
* star-fusion-gene-list-filtered.final.bedpe

FusionInspector Output
* FusionInspector candidates and fusion fragments per million mapped read values where donor and acceptor passed gene-list filter
* fusion-inspector-results.final
* *de novo* assembled transcripts using Trinity program
* FusionInspector.gmap_trinity_GG.fusions.fasta
* fusion-inspector-results.final.bedpe
* IGV input files for visualization
* FusionInspector.fa
* FusionInspector.gtf
* FusionInspector.junction_reads.bam
* FusionInspector.spanning_reads.bam

FusionInspector is configured to *de novo* assemble fusion transcripts using Trinity and to create
IGV input files for viewing fusion sequences. FusionInspector predictions with a joint FFPM > 0.1
are considered significant.
FusionInspector predictions with a joint FFPM > 0.1 are considered significant.
3 changes: 3 additions & 0 deletions star_fusion_pipeline.py
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Expand Up @@ -158,6 +158,9 @@ def fusion_inspector(results, args):
os.rename(os.path.join(fi_path, fi_output),
os.path.join(fi_path, fi_results))

# Create bedpe format
makeBedpe(fi_results, os.path.abspath('%s/fusion-inspector-results.final.bedpe' % args.output_dir))


def main():
"""
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