Reproduce_Thesis_InstitutCurie

This repository includes all code to reproduce the results from my Master's thesis named "Analyze lineage commitment during human hematopoiesis using somatic mitochondrial mutations".

Input file

The four scATAC-seq files can be downloaded using SRA toolkit from https://www.ncbi.nlm.nih.gov/sra?term=SRP256229.
Download SRR11539031.sra, SRR11539032.sra, SRR11539033.sra and SRR11539034.sra and put them in /data/sra/[sample]/[sample].sra

Set up environment

1. Install conda environment conda env create -f environment.yml
2. Install Cell Ranger ATAC https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/installation
   Install the reference data in /data/reference/refdata-cellranger-arc-GRCh38-2020-A-2.0.0
3. Install mgatk https://github.com/caleblareau/mgatk
4. Download scRNA-seq reference data for label transfer and put in /data/reference/13March2020_recluster_reannotated_10xv3.rds (https://osf.io/f5thv)

Run code

Run the bash scripts in the code folder in order 0 to 12.
Script 5 (5_Annotation_example.R) should be executed for each sample indivually, assigning identity names based on results from the label transfer.