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ChIPseq

Summary

This pipeline calls peaks in ChIP-Seq data with MACS2 and DFilter and performs motif discovery with MEME-ChIP.

The following steps are performed:

  • Read mapping with BWA aln by default. See cfg/references.yaml for default references and also refer to option --references-cfg
  • Filtering of duplicated, unmapped reads and reads with bad mapping quality (Q20).
  • By default the pipeline will call peaks with both, MACS and DFilter. This behaviour can be changed with "--skip-macs2" and "--skip-dfilter".
  • Extraction of sequences around extended peak regions followed by motif discovery with MEME-ChIP

Note, running a ChIPseq analysis requires a control and treatment sample. When using a sample config as input (--sample-cfg or -S), make sure that the control is named control.

Peak Types

The peak type is library dependent and can be set with --peak-type or -t. If set to TF or histone-narrow, MACS2 will call "narrow peaks" in either case and DFilter options will be adjusted accordingly If set to histone-broad, MACS2 will call "broad peaks" and "narrow peaks" and DFilter options will be adjusted accordingly. See the DFilter tutorial for an explanation of options.

Output

Processed BAM files (*.bwa-aln-nsrt.bam) for control and treatment samples can be found in the correspondingly named subfolders in ./out/.

Peak calling results, motif discovery results and mapping stats can be found in the ./out/treatment subfolders. The most important are

  • treatment_peaks.xls: Called peaks and peaks coordinates (MACS2 only)
  • treatment.Peaks: Called peaks and peaks coordinates (DFilter only)
  • treatment_summits.bed: Peak summit locations for every peak
  • treatment_control_lambda.bw: Control tag density profile
  • treatment_treat_pileup.bw: Treatment tag density profile
  • treatment_filtered_treatment.wig: Background smoothened treatment tag density profile (DFilter only)
  • treatment-memechip/index.html: Motif discovery results
  • treatment.bwa-aln-nsrt.bamstats/stats.txt: Mapping stats