What it does

ChIPseeker is a Bioconductor package for annotating ChIP-seq data analysis. Peak Annotation is performed by the annotatePeak function. The position and strand information of nearest genes are reported, in addition to the distance from the peak to the TSS of its nearest gene. Users can define the TSS (transcription start site) region under Advanced Options, by default the TSS region is defined from -3kb to +3kb. The genomic region of the peak is reported in the annotation column. Since some annotations may overlap for a peak, ChIPseeker adopts the following priority in genomic annotation:

• Promoter
• 5’ UTR
• 3’ UTR
• Exon
• Intron
• Downstream
• Intergenic

ChIPseeker also produces plots to help users visualise the overlaps in annotation for peaks, for example, the vennpie and upsetplot. See the ChIPseeker vignette for more information.

Inputs

A peaks file in BED, Interval or Tabular format e.g from MACS2 or DiffBind. Note that there is an option to specify if the input peaks file has a header row. No header row is assumed by default, which is usually the case for BED format e.g. MACS narrowpeak, however other formats e.g. MACS tabular format, may contain a header row.

Example:

Chrom	Start	End	Name	Score	Strand
18	394599	396513	DiffBind	0	.
18	111566	112005	DiffBind	0	.
18	346463	347342	DiffBind	0	.
18	399013	400382	DiffBind	0	.
18	371109	372102	DiffBind	0	.

A GTF file for annotation. The GTF file must have fields called "gene_id" and gene_name".

Outputs

This tool outputs

• a file of annotated peaks in Interval or Tabular format
• a PDF of plots (plotAnnoPie, plotAnnoBar, vennpie, upsetplot, plotDistToTSS)

Optionally, you can choose to output

• the R script used by this tool
• an RData file

Annotated peaks

Annotation similar to below will be added to the input file.

Example - Interval format:

Chrom	Start	End	Comment
18	394599	396513	DiffBind|0|.|Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)|1|346465|400382|53918|2|ENST00000400256| 3869|COLEC12|ENSG00000158270
18	346463	347342	DiffBind|0|.|Exon (ENST00000400256/ENSG00000158270, exon 1 of 1)|1|346465|400382|53918|2|ENST00000400256|53040|COLEC12|ENSG00000158270
18	399013	400382	DiffBind|0|.|Promoter (<=1kb)|1|346465|400382|53918|2|ENST00000400256| 0|COLEC12|ENSG00000158270
18	371109	372102	DiffBind|0|.|Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)|1|346465|400382|53918|2|ENST00000400256|28280|COLEC12|ENSG00000158270
18	111566	112005	DiffBind|0|.|Promoter (<=1kb)|1|111568|112005| 438|1|ENST00000608049| 0|ROCK1P1|ENSG00000263006

Columns contain the following data:

• Chrom: Chromosome name

• Start: Start position of site

• End: End position of site

• Comment: The pipe ("|") separated values in this column correspond to:

  • <Any additional input columns>
  • annotation (Promoter, 5’ UTR, 3’ UTR, Exon, Intron, Downstream, Intergenic)
  • geneChr
  • geneStart
  • geneEnd
  • geneLength
  • geneStrand
  • transcriptId
  • distanceToTSS
  • geneName
  • geneId

Example - Tabular format:

Chrom	Start	End	Name	Score	Strand	Comment	annotation	geneChr	geneStart	geneEnd	geneLength	geneStrand	transcriptId	distanceToTSS	geneName	geneId
18	394599	396513	DiffBind	0	.	1914|7.15|5.55|7.89|-2.35|7.06e-24|9.84e-21	Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)	1	346465	400382	53918	2	ENST00000400256	3869	COLEC12	ENSG00000158270
18	346463	347342	DiffBind	0	.	879|5|5.77|3.24|2.52|6.51e-06|0.00303	Exon (ENST00000400256/ENSG00000158270, exon 1 of 1)	1	346465	400382	53918	2	ENST00000400256	53040	COLEC12	ENSG00000158270
18	399013	400382	DiffBind	0	.	1369|7.62|7|8.05|-1.04|1.04e-05|0.00364	Promoter (<=1kb)	1	346465	400382	53918	2	ENST00000400256	0	COLEC12	ENSG00000158270
18	371109	372102	DiffBind	0	.	993|4.63|3.07|5.36|-2.3|8.1e-05|0.0226	Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)	1	346465	400382	53918	2	ENST00000400256	28280	COLEC12	ENSG00000158270
18	111566	112005	DiffBind	0	.	439|5.71|6.53|3.63|2.89|1.27e-08|8.88e-06	Promoter (<=1kb)	1	111568	112005	438	1	ENST00000608049	0	ROCK1P1	ENSG00000263006