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# Supplementary workflow details for Schuhmacher et al. 2021

This repo contains the script and documentation associated with the following publication:

**The novel Rab5 effector FERRY links the early endosome with the translation machinery**

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J. S. Schuhmacher, S. tom Dieck, S. Christoforidis, C. Landerer, L. Hersemann, S. Seifert, A. Giner, A. Toth-Petroczy, Y. Kalaizidis, E. M. Schuman, M. Zerial
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## Usage & Disclaimer
The scripts are provided as is, without the intention that an interested reader will be able to run them directly. The authors share their scripts here, not a ready-to-use tool. Still, they should provide enough technical detail to allow replicating the analyses.

Not detailed out in this repo are the steps to prepare a linux environment to include the listed tools and dependencies. Required tools include recent versions of R, samtools, STAR, bedtools, as well as:

- [ngs_tools](https://git.mpi-cbg.de/bioinfo/ngs_tools) which is a collection of deep-sequencies utilites. The version used to build the data was 73c53bdb2504166990431e6dd44f6304469544cc
- [joblist](https://git.mpi-cbg.de/bioinfo/joblist) which an HPC task manager
- [rend.R](https://git.mpi-cbg.de/bioinfo/datautils/-/tree/master/tools/rendr) which is a wrapper around knitr

## License
The scripts are provided as is under [BSD3 License](https://opensource.org/licenses/BSD-3-Clause).


## Support
For further information please contact Jan Schuhmacher ([schuhmac@mpi-cbg.de](mailto:schuhmac@mpi-cbg.de)) or [bioinformatics@mpi-cbg.de](mailto:bioinformatics@mpi-cbg.de).


## DOI
This repository is resolvable via:  https://dx.doi.org/21.11101/0000-0007-EEE3-D with the GWDG assigned (https://www.gwdg.de/en/application-services/persistent-identifier-pid/epic-pid-search) PID: 21.11101/0000-0007-EEE3-D