Peak calling workflow and Report page overview
ATAC-seq peak calling using macs2 starts with the de-duplicated BAM file produced by our alignment and QC pipeline, calls peaks, annotates peaks with genes based on proximity, provides summary statistics of the samples used in the peak-calling pipeline and an embedded genome browser to directly view all datasets combined.
Results
Peaks Distribution
-Summary plots of peak locations relative to genes
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Peaks table
-peaks called in your data with their underlying statistics and annotation of nearby genes
(detailed descriptions of the information in this table below)
Genome Browser
-an interactive, embedded IGV browser session displaying the normalized signal bigwig tracks of all samples used in the analysis
*multiple genomic loci can be visualized by specifying them with spaces in-between:
chr8:128,740,266-128,761,729 chr10:3,818,235-3,836,806 chr19:16,433,128-16,438,505
FRiP table
-Fraction of Reads in Peaks (FRiP) quantifies the enrichment of biological signal (reads) in called peaks
Enrichment
-Gene set enrichment analysis results of genes associated with peaks
(detailed descriptions of the information in this table below)
Motifs
-motifs found to be enriched in peaks and the transcription factors known to bind to the motif
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Output Files
Under the "Info" tab, intermediate files produced by the workflow can be viewed and downloaded:
MACS2
macs2/<ANALYSIS_NAME>.<genome>.macs2_peaks.xls
-raw peak calls from macs2Annotation
annotate/macs2/<ANALYSIS_NAME>.<genome>.macs2_peaks.annotated.xls
-raw peaks annotated with nearby genesannotate/macs2/<ANALYSIS_NAME>.<genome>.macs2_peaks.filtered.xls
-remaining peaks after removal of those in blacklisted regionsannotate/macs2/<ANALYSIS_NAME>.<genome>.macs2_peaks.homer_anno_raw.xls
-peaks and their annotations from the HOMER tool
ChipSeeker Docker
chip_seeker/chip_seeker/Rplots.pdf
-summary pie chart of peak annotations displaying their proximity to specific gene elements
chip_seeker/chip_seeker/covplot.png
-display of peaks along each chromosome
chip_seeker/chip_seeker/plotannopie.png
-summary pie chart of peak annotations displaying their proximity to specific gene elements
chip_seeker/chip_seeker/upsetplot.png
-upset plot of peak annotations displaying their proximity to specific gene elements
chip_seeker/chip_seeker/upsetvennpie.png
-plot combining both the pie chart and upsetplot
Enrichment
enrichment/macs2/<ANALYSIS_NAME>.<genome>.macs2_peaks.homer_anno_raw_go_summary.xls
-gene ontology enrichment results from the HOMER toolHomer
homer_view/all_motif_data.json
-json file used to display motif results in the report pagehomer_view/individual_motif_data.json
-json file used to display motif results in the report pagehomer_view/macs2/<ANALYSIS_NAME>.<genome>.macs2_peaks.filtered.motifs.zip
-compressed folder of full HOMER tool resultsBigwigSummary
multiBigwigSummary/readCounts.npz
-normalized counts in peaks for all samples used in the analysis in npz formatmultiBigwigSummary/readCounts.tab-normalized counts in peaks for all samples used in the analysis in tab-separated format