├── .__runMe.sh
├── .gitmodules
├── AnnotFilterRule.pm
├── CTAT_HumanFusionLib.mini.dat.gz
├── README.md
├── cleanMe.sh
├── minigenome.fa
├── minigenome.gtf
├── rnaseq_1.fastq.gz
└── rnaseq_2.fastq.gz


/.__runMe.sh:
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 1 | #!/bin/bash
 2 | 
 3 | set -ev
 4 | 
 5 | # prep genome lib
 6 | ../FusionFilter/prep_genome_lib.pl --genome_fa minigenome.fa --gtf minigenome.gtf --fusion_annot_lib CTAT_HumanFusionLib.mini.dat.gz --annot_filter_rule AnnotFilterRule.pm
 7 | 
 8 | # run CTAT fusion tools via the STAR-F entry point
 9 | ../STAR-Fusion --left_fq rnaseq_1.fastq.gz --right_fq rnaseq_2.fastq.gz --genome_lib_dir ctat_genome_lib_build_dir --FusionInspector validate --denovo_reconstruct
10 | 
11 | 


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/.gitmodules:
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1 | [submodule "STAR-Fusion-Tutorial.wiki"]
2 | 	path = STAR-Fusion-Tutorial.wiki
3 | 	url = https://github.com/STAR-Fusion/STAR-Fusion-Tutorial.wiki.git
4 | 


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/AnnotFilterRule.pm:
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 1 | package AnnotFilterRule;
 2 | 
 3 | ## This is a boilerplate for AnnotFilterRule
 4 | ##   which should implement rules for filtering CTAT Fusion predictions on a per-result (row) basis
 5 | ##   ideally based on the annotation field, but can be customized to liking.
 6 | 
 7 | use strict;
 8 | use warnings;
 9 | 
10 | 
11 | ####
12 | sub examine_fusion_prediction {
13 |     my ($fusion_result_row) = @_;
14 | 
15 |     #
16 |     #  $fusion_result_row has format:
17 |     #
18 |     # {
19 |     #    'LeftBreakpoint' => 'chr17:57161363:-',
20 |     #    'LeftGene' => 'TRIM37^ENSG00000108395.9',
21 |     #    'SpanningFragCount' => '3',
22 |     #    'SpanningFrags' => 'HWI-EAS418:3:83:910:1531,HWI-EAS418:6:2:1243:1560,HWI-EAS418:6:21:1070:1329',
23 |     #    'RightGene' => 'MYO19^ENSG00000141140.12',
24 |     #    'FFPM' => '795.8615',
25 |     #    'JunctionReadCount' => '1',
26 |     #    '#FusionName' => 'TRIM37--MYO19',
27 |     #    'annots' => '["CCLE","Klijn_CellLines","INTRACHROMOSOMAL[chr17:22.16Mb]"]',
28 |     #    'LeftBreakDinuc' => 'GT',
29 |     #    'LargeAnchorSupport' => 'NO_LDAS',
30 |     #    'JunctionReads' => 'HWI-EAS418:6:85:1228:1056',
31 |     #    'RightBreakDinuc' => 'AG',
32 |     #    'RightBreakEntropy' => '1.7819',
33 |     #    'SpliceType' => 'ONLY_REF_SPLICE',
34 |     #    'RightBreakpoint' => 'chr17:34863763:-',
35 |     #    'LeftBreakEntropy' => '1.7465'
36 |     # }
37 |     
38 | 
39 | 
40 |     # =============================================================
41 |     # This module should examine the contents of the 'annots' field
42 |     #   and decide whether or not to filter the prediction.
43 |     # =============================================================
44 | 
45 | 
46 |     
47 |     ## return(0) if the prediction is acceptable.
48 | 
49 |     ## return("reason for rejection")  if to be rejected.
50 |     
51 |     
52 |     return(0);  # boilerplate just accepts everything.
53 | }
54 | 
55 | 
56 | 1; #EOM
57 | 


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/CTAT_HumanFusionLib.mini.dat.gz:
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https://raw.githubusercontent.com/STAR-Fusion/STAR-Fusion-Tutorial/df8ca124e13b7abaea45162d3c2b85ceb59c5b63/CTAT_HumanFusionLib.mini.dat.gz


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/README.md:
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1 | # STAR-Fusion-Tutorial
2 | Tutorial for STAR-Fusion, FusionInspector, and de novo reconstruction of fusion transcripts using Trinity
3 | 
4 | 
5 | See the [Wiki](https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/wiki)
6 | 


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/cleanMe.sh:
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 1 | #!/bin/bash
 2 | 
 3 | rm -rf ./ctat_genome_lib_build_dir
 4 | 
 5 | rm -rf ./STAR-Fusion_outdir
 6 | 
 7 | rm -rf ./__loc_chkpts
 8 | 
 9 | rm -f ./ref_annot.cdsplus*
10 | rm -f ./ref_annot.cdna*
11 | rm -f ./pipeliner*
12 | 
13 | rm -f ./Log.out
14 | 


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/rnaseq_1.fastq.gz:
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https://raw.githubusercontent.com/STAR-Fusion/STAR-Fusion-Tutorial/df8ca124e13b7abaea45162d3c2b85ceb59c5b63/rnaseq_1.fastq.gz


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/rnaseq_2.fastq.gz:
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https://raw.githubusercontent.com/STAR-Fusion/STAR-Fusion-Tutorial/df8ca124e13b7abaea45162d3c2b85ceb59c5b63/rnaseq_2.fastq.gz


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