macs2

Model-based analysis of ChIP-seq (MACS) is a computational algorithm that identifies genome-wide locations of transcription/chromatin factor binding or histone modification from ChIP-seq data. MACS consists of four steps: removing redundant reads, adjusting read position, calculating peak enrichment and estimating the empirical false discovery rate (FDR).

ChIP comprises a few basic steps: cross-linking a protein to chromatin, shearing the chromatin, using a specific antibody to precipitate the protein of interest with its associated DNA and purifying the associated DNA fragments3.

Overview of the MACS algorithm

../../_images/macs.png

Analysis pipeline

Mapping: UNIQUE!

  • “bowtie2 -q –phred33 -k1 -p32 -x <index> -U <fastq>| -1 <r1.fastq> -2 <r2.fastq> -S <outfile>”

  • Samtools: Convert Sam to sorted Bam file (optional).