The codes contain the basic processes for ChIP-seq analysis, which contain QC, mapping, and peak calling. Narrow peak is usually for sequence-specific transcription factors, their cofactors, and, with some caveats, transcription start site or enhancer-associated histone marks. Broad peak contain certain chromatin marks (H3K9me3, H3K36me3, etc.) and chromatin proteins associated with transcriptional elongation or repression.
- Quality control: FastQC, Trimmomatic
- Mapping: BWA
- Peak calling: MACS2, BCP, MUSIC
- Annotation and visualization: ChIPseeker.
ENCODE3-pipe is a revision of ENCODE3 pipeline.