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@drpatelh drpatelh released this Jun 6, 2019 · 2 commits to master since this release

[1.0.0] - 2019-06-06

Initial release of nf-core/chipseq pipeline.


  • Raw read QC (FastQC)
  • Adapter trimming (Trim Galore!)
  • Map and filter reads (BWA, picard, SAMtools, BEDTools, BAMTools, Pysam)
  • Create library-size normalised bigWig tracks (BEDTools, bedGraphToBigWig)
  • Alignment QC metrics (Preseq, picard)
  • ChIP-seq QC metrics (deepTools, phantompeakqualtools)
  • Call and annotate broad/narrow peaks (MACS2, HOMER)
  • Create consensus set of peaks per antibody (BEDTools)
  • Quantification and differential binding analysis (featureCounts, DESeq2)
  • Collate appropriate files for genome browser visualisation (IGV)
  • Collate and present various QC metrics (MultiQC, R)
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