This repository is for the data and scripts used in the “Impact of CRISPR/HDR-editing versus lentiviral transduction on long-term engraftment and clonal dynamics of HSPCs in rhesus macaques” paper by Lee et al.
Figures 3C-E, 6A-B, 6D-E, 7A-F (Extracted Barcodes and Counts): Within “Scripts”, “BARseq_scripts_for_HDR_barcode_extraction” and “BARseq_scripts_for_LV_barcode_extraction” contain all code scripts and sample run.txt files for HDR and lentiviral genetic barcode extraction, respectively. Outputs from these scripts are merged via “merge_barseq_counts_files.R” to generate the metadata and counts files needed for input into barcodetrackR (https://github.com/dunbarlabNIH/barcodetrackR.git). “Barcode_data” provides all BARseq outputs organized by animal, and the merged BARseq metadata and counts files needed for input into barcodetrackR.