prediction of meiotic crossovers in plants
Demirci, S., Peters, S.A., Ridder, D. de and Dijk, A.D.J. van. (2018) DNA sequence and shape are predictive for meiotic crossovers throughout the plant kingdom. Plant J., 95, 686-699.
https://doi.org/10.1111/tpj.13979
- python v3.4+,
- python v2.7+,
- R v3.3.2,
- bedtools v2.25,
- fimo (MEME suite), scikit-learn, pandas, numpy, scipy, stats, matplotlib (python v3 modules),
- Bio (python module),
- DNAshapeR (R v3.3.2 package)
Tested on Ubuntu 16.04.4 LTS
bash predCO.sh [-h] [-p <true|false>] [-g <true|false>] [-n <sample_gene|genome|pericentromere] -r <reference_genome_folder> -i <input_folder> -o <output_folder> -s <path/to/scripts> -d <path/to/R-3.3.2/Rscript>