Hi-C and RNA-seq employed simultaneously (HiRES) allows us to efficiently detect both the transcriptome and the 3D genome organization in a single cell.
Linking genome structures to functions by simultaneous single-cell Hi-C and RNA-seq, Science 380, 1070–1076 (2023)
Zhiyuan Liu*; Yujie Chen*; Qimin Xia*; Menghan Liu; Heming Xu; Yi Chi; Yujing Deng; Dong Xing✉
- Raw data: PRJNA907173
- Processed data: GSE223917
This folder project contains two folders, and I will describe their respective uses below.
The HiRES_preprocess_pipeline contains a snakemake pipeline for pre-processing HiRES data.
- Place the Rawdata folder and the HiRES_preprocess_pipeline folder in the same directory.
tree -h -L 2
# .
# ├── [ 252] HiRES_preprocess_pipeline
# │ ├── [3.0K] config.yaml
# │ ├── [ 35] envs
# │ ├── [ 248] HiRES_scripts
# │ ├── [3.1K] HiRES.smk
# │ ├── [ 152] README.md
# │ ├── [ 224] rules
# │ ├── [ 361] runHiRES_preprocess.sh
# │ └── [ 20K] stat.ipynb
# └── [ 33] Rawdata
# └── [ 40] OrgfE951001 -> ../../hires_new_test/Rawdata/OrgfE951001- Installation of environment
mamba create -n hires -c conda-forge -c bioconda python=3.8 snakemake=5.20.1
mamba activate hires
mamba env update --file HiRES_preprocess_pipeline/envs/main_env.yaml- Prepare files
HiRES_preprocess_pipeline relies on hickit(https://github.com/lh3/hickit/) and CHARMtools(https://github.com/skelviper/CHARMtools) in addition to softwares that can be installed automatically. Also you need to build index for RNA/DNA seperately on your version of reference genome.
cd HiRES_preprocess_pipeline
vim config.yaml- Run the pipeline
cd HiRES_preprocess_pipeline; ./runHiRES_preprocess.sh-
generate statistics
see analysis/stat.ipynb
analysis_and_plot_notebooks holds the python/R notebooks used in the analysis of the project.