Updated: August 29, 2020
This repository contains all code needed to reproduce all analyses from this work:
C. A. Lareau*, L. S. Ludwig*, et al. Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling. Nature Biotechnology. DOI: 10.1038/s41587-020-0645-6.
Each folder corresponds to a particular dataset or analysis mode that is presented in this work. Rscripts can be found in the code folder that can be executed sequentially to reproduce analyses in part or in whole. Intermediate output files are also hosted for ease of use.
To best use this resource, we recommend pairing with large data files (that are not compatible with github as they exceed 100Mb). These files are available from the Open Science Framework.
Once one downloads the zip archieve from OSF (~36 Gb), place the extracted folder in the same directory as this repository named mtscATACpaper_large_data_files (as shown below). This will enable running custom code to reproduce items in the output folders.
.
├── mtscATACpaper_large_data_files
│ ├── intermediate
│ └── source
└── mtscATACpaper_reproducibility
├── cnv_compute
├── experimental_details
├── figure_CLL
├── figure_CRC
├── figure_invitro_CD34
├── figure_paired_cd34_pbmc
├── figures_TF1_GM11906_mixing
├── figure_supplement_public_scRNA
├── global_functions
├── numt_analysis
└── README.md
The code assumes a relative file path with this organization.
The main inputs are assumed to be output files from mgatk and CellRanger-ATAC.
For questions related to this work, please raise an issue on this repository.