JesseRop/mali22_code

Scripts and notebooks for scRNAseq analysis of Pf parasites from symptomatic and asymptomatic donors from Mali 2022 season # Mali 2022 P. falciparum single-Cell RNA-seq analysis ## Overview This repository contains code used to analyze approximately 20 asymptomatic and symptomatic *Plasmodium falciparum* infections as part of a collaboration between the Lawniczak lab at the Wellcome Sanger Institute and the Djimdes lab in the MRTC (Malaria Research and Training Center) Mali. This analysis was conducted as part of a PhD project at the University of Cambridge. Samples were processed using 10X Genomics technology as per previously published protocols and papers. Key outcomes include stage-specific transcriptomics, strain identification and differential expression (DE) between strains, and comparative analysis between symptomatic and asymptomatic infections ## Analysis summary This pipeline is designed to process 10X Genomics data from raw sequencing reads through cell calling, quality control, stage annotation, strain deconvolution, strain DE, and asymptomatic VS symptomatic analysis. Each numbered directory represents a sequential step in the analysis pipeline. ## Pipeline overview ### Stage 0: Initial preprocessing **Directory**: `0_initial_preprocessing/` Preparation of sample metadata and initial file processing, including creation of decode files for sample tracking. **Key scripts:** - `m22_decode_file_prep_jumpcode.Rmd` - Prepare sample tracking and metadata files - `m2_sympto_mdata.Rmd` - Generate symptomatic/asymptomatic metadata tables - `m2_sympto_mdata_manuscript_tables.Rmd` - Format metadata for manuscript ### Stage 1: Cell Ranger processing **Directory**: `1_cellranger/` Align sequencing reads to the *P. falciparum* reference genome and perform initial cell barcode calling using Cell Ranger. **Key scripts:** - `cellranger_count_pf_allgenes_hs_lsf_*.sh` - Submit Cell Ranger count jobs to LSF (includes human genome reference for doublet detection) - `m2_remove_HsGns_from_raw.Rmd` - Remove human genes from raw expression matrices for downstream analysis **Note**: Cel …