Transcription factor ChIP-seq Transcription factor ChIP-seq ENCODE pipeline ENCPL138KID · replicated FILE TYPE alignments ChIP-seq mapping output PEAK CALLING peak calling Phantompeakqualtools, SPP FILE TYPE peaks relaxed calls IDR IDR Irreproducible Discovery Rate FILE TYPE optimal IDR peaks thresholded peaks FILE TYPE conservative IDR thresholded peaks 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 FILE TYPE peaks conversion input FILE FORMAT CONVERSION bedToBigBed IDR peak conversion FILE TYPE bigBed converted IDR file Input and outputAnalysis stepIDRSignal generationData flow

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Components

alignments

ChIP-seq mapping output

peak calling

Phantompeakqualtools, SPP

peaks

These peak calls branch to IDR and direct bigBed conversion. Relaxed calls are not final binding sites.

IDR

Irreproducible · Discovery Rate

optimal IDR peaks

thresholded peaks

conservative IDR

thresholded peaks

bedToBigBed

peak conversion

bigBed

converted peak file

alignments

signal input

signal generation

MACS

fold change

over control

signal p-value

signal output

peaks

The ENCODE schematic draws a separate peaks input to this format-conversion step.

bedToBigBed

IDR peak conversion

bigBed

converted IDR file