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ChIP Sequencing

Domain key: chipseq

ChIP-seq identifies protein-DNA interactions genome-wide. Codaris builds pipelines covering alignment → filtering → peak calling → track generation, with blacklist filtering enforced automatically.

Step Tool Notes
QC FastQC Pre- and post-trimming
Trimming TrimGalore Adapter removal
Alignment BWA Standard for short-read ChIP
BAM processing SAMtools Filter, sort, index
Peak calling MACS2 Narrow and broad peaks
QC / tracks deepTools Cross-correlation, BigWig generation

Best Practices Enforced

  • BWA is used for alignment; multi-mapping reads are filtered (MAPQ ≥ 30)
  • ENCODE blacklist regions are filtered before peak calling — Codaris will prompt for the blacklist BED path
  • MACS2 is called with --broad for histone marks (H3K27me3, H3K9me3) and without for TFs
  • deepTools plotFingerprint and BigWig tracks are always generated for QC

Example Prompts

Build a ChIP-seq pipeline for H3K27ac in human cells.
I have IP and input control BAMs. Use GRCh38 and ENCODE blacklist.

codaris > ChIP-seq for a transcription factor — narrow peaks.
          I want cross-correlation QC and BigWig tracks for IGV.

codaris > Does my ChIP pipeline correctly handle the input control
          as a background reference in MACS2?