Update README

UCSC-Treehouse · Jan 4, 2017 · a873132 · a873132
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commit a873132
Showing 1 changed file with 24 additions and 10 deletions.
diff --git a/star-fusion/README.md b/star-fusion/README.md
@@ -5,17 +5,17 @@ STAR-Fusion for Treehouse RNA-seq analysis
 
 ### Overview
 
-Gene fusions play a major role in tumorigenesis, so it is crucial that Treehouse has a pipeline for detecting them. We have built a docker container that runs [STAR-Fusion](https://github.com/STAR-Fusion/STAR-Fusion/wiki) and filters the output against a list of known cancer fusion genes. 
+Gene fusions play a major role in tumorigenesis, so it is crucial that Treehouse has a pipeline for detecting them. We have built a docker container that runs [STAR-Fusion](https://github.com/STAR-Fusion/STAR-Fusion/wiki) and filters the output against a list of known cancer fusion genes. There is also an option to run additional filters and generate *de novo* assembled fusion transcripts using the [FusionInspector](https://github.com/FusionInspector/FusionInspector/wiki/Home/5fb0116687e9f80a7e926e55657b46392b781f64) program.
 
 ### Docker and usage
 
 ##### Image located on hub.docker.com
 
 REPOSITORY: jpfeil/star-fusion
 
-TAG: 0.0.1
+TAG: 0.0.2
 
-IMAGE ID: 520e7a15847b
+IMAGE ID: bb0c8be35574
 
 
 ##### Input files
@@ -26,9 +26,9 @@ The pipeline requires paired-end fastq files, the output directory, and the geno
 usage: star_fusion_pipeline.py [-h] --left_fq R1 --right_fq R2 --output_dir
                                OUTPUT_DIR --genome_lib_dir GENOME_LIB_DIR
                                [--CPU CPU] [--genelist GENELIST]
-                               [--skip_filter] [--test]
+                               [--skip_filter] [-F] [--test]
 
-Wraps STAR-Fusion program and filters output.
+Wraps STAR-Fusion program and filters output using FusionInspector.
 
 optional arguments:
   -h, --help            show this help message and exit
@@ -41,8 +41,9 @@ optional arguments:
   --CPU CPU             Number of cores
   --genelist GENELIST
   --skip_filter
+  -F, --run_fusion_inspector
+                        Runs FusionInspector on output
   --test
-
 ```
 
 
@@ -54,13 +55,26 @@ docker run -it --rm -v `pwd`:/data jpfeil/star-fusion:0.0.1 \
                                    --output_dir fusion_output \
                                    --CPU `nproc` \
                                    --genome_lib_dir STARFusion-GRCh38gencode23
+                                   --run_fusion_inspector
 ```
 
 ### **Output**
 
-There will be many files in the output directory, but you can find the fusion calls in these files:
+There will be many files in the output directory, but you can find the fusion calls here:
+
+- `star-fusion.fusion_candidates.final.abridged.FFPM`
+- `star-fusion.fusion_candidates.final.in_genelist.abridged.FFPM`
+
+The second file contains fusion calls where both fusion partners are in the gene-list. If the pipeline is run with the --run_fusion_inspector flag, then there will also be a separate FusionInspector directory that contains fusion calls that passed the FusionInspector filter. FusionInspector is also configured to *de novo* assemble fusion transcripts using Trinity and to create IGV input files for viewing fusion sequences.
 
-- `star-fusion.fusion_candidates.final.abridged`
-- `star-fusion.fusion_candidates.final.in_genelist.abridged`
+* FusionInspector predictions 
+  * `FusionInspector/FusionInspector.fusion_predictions.final.abridged.FFPM`
+* *de novo* assembled transcripts
+  * `FusionInspector/FusionInspector.gmap_trinity_GG.fusions.fasta`
+* IGV input files
+  * `FusionInspector/FusionInspector.fa`
+  * `FusionInspector/FusionInspector.gtf`
+  * `FusionInspector/FusionInspector.junction_reads.bam`
+  * `FusionInspector/FusionInspector.spanning_reads.bam`
 
-The second file contains fusion calls were both fusion partners are in the genelist.
+FusionInspector predictions with a combined FFPM > 0.1 are considered significant.