Transposable elements contribute to cell and species-specific looping diversity and gene expression in mammalian genomes.

This repository can be used to reproduce source data and results contributing to all figures and tables presented in:

Diehl AG, Ouyang N, and Boyle AP. Transposable elements contribute to cell and species-specific looping diversity and gene expression in mammalian genomes. Nature Com. (2020)

Instructions

All resources used to preprocess the source datasets are housed in the data directory. Each subdirectory contains a README file with links and processing steps to prepare the source data. This must be completed prior to running any of the main analysis steps.

The remaining folders loosely correspond to the results sections/figures presented within the main text. Because the analyses build on each other, it is recommended to perform analyses in the following order:

1. TE-CTCF-Orth
2. TE-CTCF-Enrichment
3. TE-Loop-Intersection
4. Loop-Conservation
5. Gene-Expression

Some analyses include results of hadoop/hive queries. All code to reproduce the data tables and queries is included for those with access to a hadoop cluster. Full, unprocessed query results are included in the data/hadoop/results directory for those lacking access to suitable computing resources.

Dependencies

Software tools required to run this analysis are described in the "Code Availability" section of the manuscript. These shoudl be retrieved directly from their respective repositories/web sites/authors. All remaining custom code referenced in the manuscript is provided within this repository.

Perl scripts included in this repository may require installation of additional non-default modules in order to run properly. Known dependencies are listed below. Please let us know if we have missed any!

1. Getopt::Long
2. Bio::Seq
3. Bio::SeqIO
4. threads

Python scripts included in this repository may also include non-default dependencies. It is recommended to run all python scripts within a Conda environment using Python 3.6.9. Known dependencies are listed below. Please let us know if we have missed any!

1. pandas
2. numpy
3. tabix

Questions and Bug Reports

Please contact Adam Diehl (adadiehl@umich.edu) with technical questions/bug reports.