Code for MNase-seq and ChIP-seq analysis

Code used for the analysis of MNase-seq and ChIP-seq data from the publication "In vitro reconstitution of chromatin domains shows a role for nucleosome positioning in 3D genome organization".

1. Map fastq files with "fastq2bam.sh" to the SacCer3 genome. Prerequisite: Install bowtie, samtool and download the SacCer3 Bowtie indices.

2. MNase-seq: Import bam files into R with "MNase-seq-data-analysis.rmd", convert them to bigwig files and align them at +1 nucleosome positions or Reb1- or Abf1-binding sites from "Alignments_for_pGPV_X.rds" for Chr5-10 or "Alignments_for_pGP.rds" for all Chromosomes. Aligned data is saved and can be used to plot pile-up plots or to call nucleosome peaks and plot linker length etc. (in "MNase-seq-data-analysis.rmd").

3a.ChIP-seq: Import bam files into R with "ChIP-seq.R" and plot either heatmaps or composite plots of ChIP or MNase-seq data (Input). Heatmaps are sorted by in vivo Abf1 or Reb1 binding (e.g. "Sorted-Reb1-SLIM-ChIP-gene.rda").

3b. Call peaks from ChIP bam files with MACS2 and identify PWM motif in the peaks with MEME (ChIP-seq_MACS2-MEME.sh).