ATAC-Seq macs2 peak analysis

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

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

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