Wheat DMC1 and ASY1 ChIP-seq custom scripts

This repository contains custom scripts used in the preparation of the paper entitled “Crossover-active regions of the wheat genome are distinguished by DMC1, the chromosome axis, H3K27me3 and signatures of adaptation” by Andrew J. Tock, Daniel M. Holland, Wei Jiang, Kim Osman, Eugenio Sanchez-Moran, James D. Higgins, Keith J. Edwards, Cristobal Uauy, F. Chris H. Franklin and Ian R. Henderson.

These files can be downloaded together by cloning the repository, which requires git:

git clone https://github.com/ajtock/Wheat_DMC1_ASY1_paper/

Alternatively, individual files (e.g., Snakefile) can be downloaded using wget:

wget https://raw.githubusercontent.com/ajtock/Wheat_DMC1_ASY1_paper/scripts/read_alignment/snakemake_ChIPseq_MNaseseq/Snakefile

Alignment workflows

Workflows for processing and aligning next-generation sequencing (NGS) reads were developed using Snakemake v3.13.3 in conjunction with conda v4.6.9 package and environment manager. These workflows are located in scripts/read_alignment/ in this repository.

Feature analyses

Scripts for analyzing ChIP-seq peaks and genes are located in scripts/ChIPseq_peaks/ and scripts/genes/.

Chromosome profiles

Scripts for calculating and plotting windowed library-size-normalized log2(ChIP/control) coverage, recombination rate (cM/Mb), and feature frequency along the wheat chromosomes are located in scripts/chromosomes/.

Chromosome compartments

Previously defined coordinates delimiting compartments of the chromosomes of hexaploid wheat landrace Chinese Spring are detailed in chromosome_compartments/.