Code for MNase-seq and ChIP-seq analysis
Description
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).
Files
Files
(315.9 kB)
Name | Size | Download all |
---|---|---|
md5:9f841a27be0e4c0b7479c960d25118c2
|
227.5 kB | Download |
md5:db7280f978fbb86faff6fa9889d8aedf
|
22.7 kB | Download |
md5:962990506f5f813dd0cfd1a2a55c1382
|
13.2 kB | Download |
md5:d0d5d1d9bc5d5e81b228d1c4fcb83096
|
515 Bytes | Download |
md5:de31103a8d96d443401fcf11c61c87cc
|
275 Bytes | Download |
md5:55dfcb8c4571454360ae9783114a3b1e
|
16.0 kB | Download |
md5:fa9fe802aa4ff188e74570a2083573ae
|
17.8 kB | Download |
md5:242323f96e67c8c94ee703afdbc167ca
|
17.8 kB | Download |