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Route: chip

ChIP-seq analysis.


  • Align to the reference genome (Bowtie2).
  • Remove duplicate reads (Sambamba).
  • Generate genome browser tracks.

For peak calling, follow with chip-pairs-peaks.


Set up a new analysis (common across all routes). If running for the first time, check the detailed usage instructions for an explanation of every step.

cd <project dir>
git clone --depth 1
sns/generate-settings <genome>
sns/gather-fastqs <fastq dir>

Run chip route.

sns/run chip

Check for potential problems.

grep "ERROR:" logs-sbatch/*


Primary results:

  • BAM-DD: Deduplicated BAM files. Can be used for additional analysis.
  • BIGWIG: BigWig files normalized to the total number of reads. Can be used for visual inspection of peaks.

Run metrics:

  • summary-combined.chip.csv: Summary table that includes the number of reads, alignment rate, and fraction of PCR duplicates.