KdmB-EcoA-RpdA-SntB (KERS) chromatin complex ChIPseq data analysis

KERS is a tetrameric nucleosome remodelling complex in the filamentous fungus Aspergillus nidulans that is composed of the H3K4 histone demethylase KdmB, a cohesin acetyltransferase (EcoA), a histone deacetylase (RpdA) and a reader protein (SntB). This repository has the scripts related to KERS ChIPseq data analysis.

Required tools for data analysis

A. nidulans AnnotationHub packages like `org.db`, `TxDb` and `BSgenome`

## org.db
devtools::install_github(
  "lakhanp1/fungal_resources/A_nidulans/org.Anidulans.FGSCA4.eg.db",
  upgrade = "never")
  
## TxDb
devtools::install_github(
  "lakhanp1/fungal_resources/A_nidulans/TxDb.Anidulans.FGSCA4.AspGD.GFF",
  upgrade = "never")
  
## BSgenome
devtools::install_github(
  "lakhanp1/fungal_resources/A_nidulans/BSgenome.Anidulans.FGSCA4.AspGD",
  upgrade = "never")

R package `chipmine` with utility functions for ChIPseq data management and processing

chipmine is under active development. For the analysis involving current manuscript, chimpine from branch KERS_paper was used.

devtools::install_github(repo = "lakhanp1/chipmine", ref = "KERS_paper")

Data processing

All the ChIPseq data was processed as per steps mentioned in fungal ChIPseq data processing workflow of Koon Ho Wong lab.

Data Availability

NCBI SRA data: ChIPseq raw data is deposited to NCBI SRA Bioproject PRJNA591094.

UCSC genome browser tracks: All the normalized bigWig tracks for ChIPseq data are made available on UCSC genome browser and can be accessed using link https://genome-asia.ucsc.edu/s/lakhanp1/A.%20nidulans%20KERS

lakhanp1/KERS_project