Bioinformatics Core Workflow for ChIP-Seq Data Analysis.
Tamás SchauerPublished in: Methods in molecular biology (Clifton, N.J.) (2024)
Chromatin immunoprecipitation (ChIP) followed by next-generation sequencing (-seq) has been the most common genomics method for studying DNA-protein interactions in the last decade. ChIP-seq technology became standard both experimentally and computationally. This chapter presents a core workflow that covers data processing and initial analytical steps of ChIP-seq data. We provide a step-by-step protocol of the commands as well as a fully assembled Snakemake workflow. Along the protocol, we discuss key tool parameters, quality control, output reports, and preliminary results.
Keyphrases
- single cell
- data analysis
- high throughput
- genome wide
- electronic health record
- rna seq
- circulating tumor cells
- quality control
- circulating tumor
- randomized controlled trial
- dna methylation
- copy number
- big data
- gene expression
- dna damage
- emergency department
- transcription factor
- cell free
- small molecule
- protein protein
- deep learning
- liquid chromatography
- artificial intelligence
- amino acid