mtinti/VSG_Competition

Code for the paper Competition among variants is predictable and controls the antigenic variation dynamics of African trypanosomes in cell culture # VSG Competition Code for the paper Competition among variants is predictable and controls the antigenic variation dynamics of African trypanosomes in cell culture Code to align and count reads ## *Project Description* We induced VSG gene recombination and switching in in vitro culture using CRISPR-Cas9 nuclease to target the active VSG We conclude that antigenic variants compete, and that the population of cells that activates minichromosome derived VSGs displays a competitive advantage. Competition among variants impacts antigenic variation dynamics in African trypanosomes and likely prolongs immune evasion with a limited set of antigens. ### *Files Description* - env.version.txt -> conda packages - template_rnaseq-def.sh -> template file to align fastq files and count VSGs - experiment_1 -> dataset for main data in paper - experiment_2 -> dataset to address reviewer comments