Transcription factor ChIP-seq (unreplicated) Transcription factor ChIP-seq (unreplicated) ENCODE pipeline ENCPL493SGC · pseudoreplicate IDR FILE TYPE alignments ChIP-seq mapping output PEAK CALLING peak calling Phantompeakqualtools, SPP FILE TYPE peaks relaxed calls UNREPLICATED IDR unreplicated IDR Irreproducible Discovery Rate FILE TYPE pseudoreplicated IDR thresholded peaks FILE FORMAT CONVERSION bedToBigBed IDR peak conversion FILE TYPE bigBed converted IDR file FILE FORMAT CONVERSION bedToBigBed peak conversion FILE TYPE bigBed converted peak file FILE TYPE alignments signal input SIGNAL GENERATION signal generation MACS FILE TYPE fold change over control FILE TYPE signal p-value signal output Input and outputAnalysis stepUnreplicated IDRSignal generationData flow

Drag to pan · ⌘/Ctrl + scroll to zoom · F to fit

Components

alignments

ChIP-seq mapping output

peak calling

Phantompeakqualtools, SPP

peaks

relaxed calls

unreplicated IDR

This step evaluates pseudoreplicates, not independent biological replicates.

pseudoreplicated

IDR thresholded peaks

bedToBigBed

IDR peak conversion

bigBed

converted IDR file

bedToBigBed

peak conversion

bigBed

converted peak file

alignments

signal input

signal generation

MACS

fold change

over control

signal p-value

signal output