├── .gitignore ├── CITATION.cff ├── README.md ├── docs ├── about │ └── index.html ├── contact │ └── index.html ├── css │ ├── blackburn.css │ ├── side-menu-old-ie.css │ └── side-menu.css ├── img │ └── favicon.ico ├── index.html ├── index.xml ├── js │ ├── menus.js │ └── ui.js ├── page │ └── 1 │ │ └── index.html ├── post │ ├── creating-a-new-theme │ │ └── index.html │ ├── index.html │ ├── index.xml │ └── migrate-from-jekyll │ │ └── index.html ├── sitemap.xml ├── tags │ ├── index.html │ └── index.xml └── topics │ ├── index.html │ └── index.xml ├── img ├── approach.png ├── compositionAssociation.png └── workflow.png ├── setup.py ├── src └── truster │ ├── __init__.py │ ├── __pycache__ │ ├── __init__.cpython-37.pyc │ ├── bcolors.cpython-37.pyc │ └── jobHandler.cpython-37.pyc │ ├── bcolors.py │ ├── cluster.py │ ├── experiment.py │ ├── jobHandler.py │ ├── py_scripts │ ├── concatenate_fastqs.py │ ├── filterUMIs │ ├── plotTEexpression │ ├── plotVelocity │ └── plotVelocity.py │ ├── r_scripts │ ├── get_clusters.R │ ├── merge_samples.R │ └── normalize_TEexpression.R │ └── sample.py └── test ├── 3_merge_samples ├── cluster_pipeline │ └── bam_to_fastq │ │ ├── sample_A │ │ ├── sample_A_merged.clusters_0 │ │ │ ├── sample_A_0_1_libraryA │ │ │ │ ├── bamtofastq_S1_L001_R2_001.fastq.gz │ │ │ │ ├── bamtofastq_S1_L002_R2_001.fastq.gz │ │ │ │ ├── bamtofastq_S1_L003_R2_001.fastq.gz │ │ │ │ └── bamtofastq_S1_L004_R2_001.fastq.gz │ │ │ └── sample_A_0_1_libraryB │ │ │ │ ├── bamtofastq_S1_L001_R2_001.fastq.gz │ │ │ │ ├── bamtofastq_S1_L002_R2_001.fastq.gz │ │ │ │ ├── bamtofastq_S1_L003_R2_001.fastq.gz │ │ │ │ └── bamtofastq_S1_L004_R2_001.fastq.gz │ │ └── sample_A_merged.clusters_1 │ │ │ ├── sample_A_0_1_libraryA │ │ │ ├── bamtofastq_S1_L001_R2_001.fastq.gz │ │ │ ├── bamtofastq_S1_L002_R2_001.fastq.gz │ │ │ ├── bamtofastq_S1_L003_R2_001.fastq.gz │ │ │ └── bamtofastq_S1_L004_R2_001.fastq.gz │ │ │ └── sample_A_0_1_libraryB │ │ │ ├── bamtofastq_S1_L001_R2_001.fastq.gz │ │ │ ├── bamtofastq_S1_L002_R2_001.fastq.gz │ │ │ ├── bamtofastq_S1_L003_R2_001.fastq.gz │ │ │ └── bamtofastq_S1_L004_R2_001.fastq.gz │ │ ├── sample_B │ │ ├── sample_B_merged.clusters_0 │ │ │ └── sample_B_0_1_libraryA │ │ │ │ ├── bamtofastq_S1_L001_R2_001.fastq.gz │ │ │ │ ├── bamtofastq_S1_L002_R2_001.fastq.gz │ │ │ │ ├── bamtofastq_S1_L003_R2_001.fastq.gz │ │ │ │ └── bamtofastq_S1_L004_R2_001.fastq.gz │ │ └── sample_B_merged.clusters_1 │ │ │ └── sample_B_0_1_libraryA │ │ │ ├── bamtofastq_S1_L001_R2_001.fastq.gz │ │ │ ├── bamtofastq_S1_L002_R2_001.fastq.gz │ │ │ ├── bamtofastq_S1_L003_R2_001.fastq.gz │ │ │ └── bamtofastq_S1_L004_R2_001.fastq.gz │ │ └── sample_C │ │ ├── sample_C_merged.clusters_0 │ │ └── sample_C_0_1_libraryA │ │ │ ├── bamtofastq_S1_L001_R2_001.fastq.gz │ │ │ ├── bamtofastq_S1_L002_R2_001.fastq.gz │ │ │ ├── bamtofastq_S1_L003_R2_001.fastq.gz │ │ │ └── bamtofastq_S1_L004_R2_001.fastq.gz │ │ └── sample_C_merged.clusters_1 │ │ └── sample_C_0_1_libraryA │ │ ├── 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