cyberneticlibrary
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Execute ChIP-seq data processing pipelines

pipeline-chipseqskillsetup L4★35
ammawla/encode-toolkit ↗
What it does

Execute ENCODE ChIP-seq processing pipeline from FASTQ

Best for

Processing ChIP-seq data with treatment/control comparisons and IDR replicate analysis.

Inputs
  • · FASTQ files (paired-end or single-end)
  • · Aligned BAM files
  • · Reference genome (indexed)
  • · Sample metadata sheet (CSV)
Outputs
  • · Peak calls (narrowPeak/broadPeak format)
  • · Signal tracks (bigWig)
  • · Quality control report
Requires
  • · Nextflow
  • · Docker
  • · BWA/Bowtie2 aligner
  • · MACS2 peak caller
  • · IDR (irreproducible discovery rate)
Preconditions
  • · Reference genome indexed
  • · FASTQ files available
  • · Nextflow/Docker installed
Failure modes
  • · Poor FASTQ quality (low pass rate)
  • · Reference genome mismatch
  • · Memory exhaustion on large datasets
  • · Adapter contamination
Trust signals
  • · ENCODE consortium standards documented
  • · Maintained in ammawla/encode-toolkit
  • · Peer-reviewed publications cited