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friedue authored Jun 17, 2019
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# TOX is a critical regulator of tumour-specific T cell differentiation

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*.](https://www.nature.com/articles/s41586-019-1324-y).
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*.](https://www.nature.com/articles/s41586-019-1324-y)

All scripts were written by Paul Zumbo and Friederike Duendar.

See the [Methods](https://github.com/friedue/Scott2019/blob/master/methods_andrew.md) for a verbose description of the processing steps.
The individual scripts can be found in the respective folders of this repository where [preprocessing](https://github.com/friedue/Scott2019/tree/master/preprocessing) contains the makefiles for the QC, alignment and analysis of both RNA-seq and ATAC-seq data while
[the other folder](https://github.com/friedue/Scott2019/tree/master/code_for_figures) 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.
Don't hesitate to [get in touch](https://abc.med.cornell.edu/) with questions related to the code.

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