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Clindet documentation
Contents:
Quick Start
1. Clindet
2. Setup Clindet
3. Use case
DNAseq analysis
1. Whole exome sequence data analysis
1.1. ClinDet WXS workflow
2. Whole genome sequence data analysis
2.1. ClinDet WGS workflow
RNAseq analysis
1. ClinDet RNA-seq workflow
Use Case
1. Use case I: SNV and CNV calling from
Whole exome sequencing
data
2. Use case II: Fusion genes detection from
multiple myeloma patient
RNA-seq
3. Use case III: Whole genome sequencing of
COLO829 cell line
4. Use case IV: Quantifying the contributions of DNA repair defective gene mutations to mutational signatures（
C.elegans
）
5. Use case V: Switching to different genome version (e.g. hg38)
A Gym for Clinical NGS Data Analysis Workflows
1. Clinical Omics Benchmark Datasets
2. Benchmark
snakemake/clindet: Citations
.rst
.pdf
RNAseq analysis
RNAseq analysis
#
1. ClinDet RNA-seq workflow
