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update doctoc
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allyhawkins committed Jun 3, 2022
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- [Reference files and general setup](#reference-files-and-general-setup)
- [GoT-Splice Pipeline overview](#got-splice-pipeline-overview)
- [Junction Calling in Single Cells](#junction-calling-in-single-cells)
- [Annotation of Intron Junctions](#annotation-of-intron-junctions)
- [Annotation of Junctions](#annotation-of-junctions)
- [Differential Transcript Usage](#differential-transcript-usage)
- [Option A: Individual Patient](#option-a-individual-patient)
- [Option A: Individual Samples](#option-a-individual-samples)
- [Option B: Combine Samples](#option-b-combine-samples)
- [Option C: Within Cell Types/ Clusters](#option-c-within-cell-types-clusters)
- [Running the full GoT-Splice pipeline](#running-the-full-got-splice-pipeline)
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