Collection of scripts used for the processing and analysis of high-throughput sequencing data (RNA-seq and ATAC-seq) for Scott et al., 2019 (Nature). TOX is a critical regulator of tumour-specific T cell differentiation.

All scripts were written by Paul Zumbo and Friederike Dündar.

See the Methods for a verbose description of the processing steps.

The individual scripts can be found in the respective folders of this repository where preprocessing contains the makefiles for the QC, alignment and analysis of both RNA-seq and ATAC-seq data while the other folder contains the Rmarkdown documents that will help you understand how the individual figures using RNA-seq and ATAC-seq data were generated.

The raw data was submitted to GEO: GSE126974.

Don't hesitate to get in touch with questions related to the code.