ChIP-Seq Pipeline summary

Raw read QC (FastQC)
Adapter trimming (Trim Galore!)
Alignment (BWA)
Mark duplicates (picard)
Merge alignments from multiple libraries of the same sample (picard)
1. Re-mark duplicates (picard)
2. Filtering to remove: reads mapping to blacklisted regions (SAMtools, BEDTools)
  reads that are marked as duplicates (SAMtools)
  reads that arent marked as primary alignments (SAMtools)
  reads that are unmapped (SAMtools)
  reads that map to multiple locations (SAMtools)
  reads containing > 4 mismatches (BAMTools)
  reads that have an insert size > 2kb (BAMTools)
  reads that map to different chromosomes (Pysam)
  reads that arent in FR orientation (Pyssam) reads where only one read of the pair fails the above criteria (Pysam)
Alignment-level QC and estimation of library complexity (picard, Preseq)\
Create normalised bigWig files scaled to 1 million mapped reads (BEDTools, bedGraphToBigWig)
Generate gene-body meta-profile from bigWig files (deepTools)
Calculate genome-wide IP enrichment relative to control (deepTools)
Calculate strand cross-correlation peak and ChIP-seq quality measures including NSC and RSC (phantompeakqualtools)
Call broad/narrow peaks (MACS2)

Multi-QC explanation

https://nf-co.re/chipseq/1.2.1/output

Phantompeakqualtools

Calculate strand cross-correlation peak and ChIP-seq quality measures

Publications

https://pubmed.ncbi.nlm.nih.gov/22955991/ https://www.nature.com/articles/nbt.1508

cross-correlation peak strandshift figures

./bwa/mergedLibrary/phantompeakqualtools/3xHA-HD-like_R3.spp.pdf
./bwa/mergedLibrary/phantompeakqualtools/HD-like-3xHA_R1.spp.pdf
./bwa/mergedLibrary/phantompeakqualtools/NFYB3-3xHA_R3.spp.pdf
./bwa/mergedLibrary/phantompeakqualtools/NFYB3-3xHA_R2.spp.pdf
./bwa/mergedLibrary/phantompeakqualtools/NFYB3-3xHA_R1.spp.pdf
./bwa/mergedLibrary/phantompeakqualtools/3xHA_R3.spp.pdf
./bwa/mergedLibrary/phantompeakqualtools/3xHA-HD-like_R2.spp.pdf
./bwa/mergedLibrary/phantompeakqualtools/3xHA-MYB59_R3.spp.pdf
./bwa/mergedLibrary/phantompeakqualtools/3xHA_R2.spp.pdf
./bwa/mergedLibrary/phantompeakqualtools/3xHA-NFYB3_R2.spp.pdf
./bwa/mergedLibrary/phantompeakqualtools/HD-like-3xHA_R3.spp.pdf
./bwa/mergedLibrary/phantompeakqualtools/3xHA-NFYB3_R1.spp.pdf
./bwa/mergedLibrary/phantompeakqualtools/3xHA-HD-like_R1.spp.pdf
./bwa/mergedLibrary/phantompeakqualtools/MYB59-3xHA_R2.spp.pdf
./bwa/mergedLibrary/phantompeakqualtools/3xHA-MYB59_R2.spp.pdf
./bwa/mergedLibrary/phantompeakqualtools/3xHA_R1.spp.pdf
./bwa/mergedLibrary/phantompeakqualtools/3xHA-NFYB3_R3.spp.pdf
./bwa/mergedLibrary/phantompeakqualtools/MYB59-3xHA_R3.spp.pdf
./bwa/mergedLibrary/phantompeakqualtools/HD-like-3xHA_R2.spp.pdf
./bwa/mergedLibrary/phantompeakqualtools/MYB59-3xHA_R1.spp.pdf
./bwa/mergedLibrary/phantompeakqualtools/3xHA-MYB59_R1.spp.pdf

Picard

Mark duplicate; Merge alignments from multiple libraries of the same sample

Introduction

https://www.broadinstitute.org/files/shared/mpg/plathumgen/plathumgen_fennell.pdf

Citation

“Picard Toolkit.” 2018. Broad Institute, GitHub Repository. http://broadinstitute.github.io/picard/; Broad Institute

QC and metic plots

./bwa/mergedLibrary/picard_metrics/pdf/HD-like-3xHA_R1.mLb.clN.CollectMultipleMetrics.base_distribution_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-MYB59_R1.mLb.clN.CollectMultipleMetrics.quality_distribution.pdf
./bwa/mergedLibrary/picard_metrics/pdf/MYB59-3xHA_R1.mLb.clN.CollectMultipleMetrics.quality_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA_R3.mLb.clN.CollectMultipleMetrics.base_distribution_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-MYB59_R3.mLb.clN.CollectMultipleMetrics.insert_size_histogram.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-MYB59_R2.mLb.clN.CollectMultipleMetrics.quality_distribution.pdf
./bwa/mergedLibrary/picard_metrics/pdf/HD-like-3xHA_R2.mLb.clN.CollectMultipleMetrics.insert_size_histogram.pdf
./bwa/mergedLibrary/picard_metrics/pdf/HD-like-3xHA_R1.mLb.clN.CollectMultipleMetrics.quality_distribution.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA_R1.mLb.clN.CollectMultipleMetrics.base_distribution_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-NFYB3_R1.mLb.clN.CollectMultipleMetrics.quality_distribution.pdf
./bwa/mergedLibrary/picard_metrics/pdf/MYB59-3xHA_R1.mLb.clN.CollectMultipleMetrics.base_distribution_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/NFYB3-3xHA_R2.mLb.clN.CollectMultipleMetrics.quality_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/NFYB3-3xHA_R2.mLb.clN.CollectMultipleMetrics.quality_distribution.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-HD-like_R2.mLb.clN.CollectMultipleMetrics.quality_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/MYB59-3xHA_R3.mLb.clN.CollectMultipleMetrics.quality_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA_R2.mLb.clN.CollectMultipleMetrics.quality_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA_R2.mLb.clN.CollectMultipleMetrics.base_distribution_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/MYB59-3xHA_R2.mLb.clN.CollectMultipleMetrics.quality_distribution.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-HD-like_R3.mLb.clN.CollectMultipleMetrics.quality_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-NFYB3_R1.mLb.clN.CollectMultipleMetrics.quality_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/HD-like-3xHA_R3.mLb.clN.CollectMultipleMetrics.quality_distribution.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA_R1.mLb.clN.CollectMultipleMetrics.quality_distribution.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-MYB59_R1.mLb.clN.CollectMultipleMetrics.base_distribution_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA_R1.mLb.clN.CollectMultipleMetrics.quality_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/NFYB3-3xHA_R1.mLb.clN.CollectMultipleMetrics.base_distribution_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/MYB59-3xHA_R2.mLb.clN.CollectMultipleMetrics.insert_size_histogram.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-MYB59_R3.mLb.clN.CollectMultipleMetrics.quality_distribution.pdf
./bwa/mergedLibrary/picard_metrics/pdf/HD-like-3xHA_R2.mLb.clN.CollectMultipleMetrics.quality_distribution.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA_R3.mLb.clN.CollectMultipleMetrics.insert_size_histogram.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-MYB59_R1.mLb.clN.CollectMultipleMetrics.quality_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/MYB59-3xHA_R2.mLb.clN.CollectMultipleMetrics.base_distribution_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/NFYB3-3xHA_R2.mLb.clN.CollectMultipleMetrics.insert_size_histogram.pdf
./bwa/mergedLibrary/picard_metrics/pdf/HD-like-3xHA_R2.mLb.clN.CollectMultipleMetrics.quality_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/MYB59-3xHA_R3.mLb.clN.CollectMultipleMetrics.insert_size_histogram.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-NFYB3_R2.mLb.clN.CollectMultipleMetrics.base_distribution_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/HD-like-3xHA_R1.mLb.clN.CollectMultipleMetrics.quality_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-NFYB3_R2.mLb.clN.CollectMultipleMetrics.quality_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-MYB59_R2.mLb.clN.CollectMultipleMetrics.insert_size_histogram.pdf
./bwa/mergedLibrary/picard_metrics/pdf/MYB59-3xHA_R3.mLb.clN.CollectMultipleMetrics.base_distribution_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-HD-like_R2.mLb.clN.CollectMultipleMetrics.insert_size_histogram.pdf
./bwa/mergedLibrary/picard_metrics/pdf/MYB59-3xHA_R3.mLb.clN.CollectMultipleMetrics.quality_distribution.pdf
./bwa/mergedLibrary/picard_metrics/pdf/NFYB3-3xHA_R1.mLb.clN.CollectMultipleMetrics.quality_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA_R3.mLb.clN.CollectMultipleMetrics.quality_distribution.pdf
./bwa/mergedLibrary/picard_metrics/pdf/NFYB3-3xHA_R3.mLb.clN.CollectMultipleMetrics.quality_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-HD-like_R1.mLb.clN.CollectMultipleMetrics.quality_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-HD-like_R1.mLb.clN.CollectMultipleMetrics.insert_size_histogram.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA_R2.mLb.clN.CollectMultipleMetrics.quality_distribution.pdf
./bwa/mergedLibrary/picard_metrics/pdf/NFYB3-3xHA_R1.mLb.clN.CollectMultipleMetrics.insert_size_histogram.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-NFYB3_R3.mLb.clN.CollectMultipleMetrics.quality_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/HD-like-3xHA_R1.mLb.clN.CollectMultipleMetrics.insert_size_histogram.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-MYB59_R3.mLb.clN.CollectMultipleMetrics.quality_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/HD-like-3xHA_R3.mLb.clN.CollectMultipleMetrics.base_distribution_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-HD-like_R1.mLb.clN.CollectMultipleMetrics.base_distribution_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/HD-like-3xHA_R3.mLb.clN.CollectMultipleMetrics.insert_size_histogram.pdf
./bwa/mergedLibrary/picard_metrics/pdf/NFYB3-3xHA_R1.mLb.clN.CollectMultipleMetrics.quality_distribution.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-MYB59_R1.mLb.clN.CollectMultipleMetrics.insert_size_histogram.pdf
./bwa/mergedLibrary/picard_metrics/pdf/HD-like-3xHA_R3.mLb.clN.CollectMultipleMetrics.quality_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-NFYB3_R1.mLb.clN.CollectMultipleMetrics.insert_size_histogram.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-HD-like_R3.mLb.clN.CollectMultipleMetrics.insert_size_histogram.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-HD-like_R3.mLb.clN.CollectMultipleMetrics.base_distribution_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-NFYB3_R3.mLb.clN.CollectMultipleMetrics.base_distribution_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-MYB59_R2.mLb.clN.CollectMultipleMetrics.base_distribution_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-HD-like_R3.mLb.clN.CollectMultipleMetrics.quality_distribution.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-NFYB3_R2.mLb.clN.CollectMultipleMetrics.quality_distribution.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-HD-like_R2.mLb.clN.CollectMultipleMetrics.base_distribution_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/MYB59-3xHA_R2.mLb.clN.CollectMultipleMetrics.quality_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-HD-like_R1.mLb.clN.CollectMultipleMetrics.quality_distribution.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA_R1.mLb.clN.CollectMultipleMetrics.insert_size_histogram.pdf
./bwa/mergedLibrary/picard_metrics/pdf/MYB59-3xHA_R1.mLb.clN.CollectMultipleMetrics.quality_distribution.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-MYB59_R2.mLb.clN.CollectMultipleMetrics.quality_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-NFYB3_R3.mLb.clN.CollectMultipleMetrics.quality_distribution.pdf
./bwa/mergedLibrary/picard_metrics/pdf/HD-like-3xHA_R2.mLb.clN.CollectMultipleMetrics.base_distribution_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-MYB59_R3.mLb.clN.CollectMultipleMetrics.base_distribution_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA_R3.mLb.clN.CollectMultipleMetrics.quality_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/NFYB3-3xHA_R2.mLb.clN.CollectMultipleMetrics.base_distribution_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-HD-like_R2.mLb.clN.CollectMultipleMetrics.quality_distribution.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-NFYB3_R3.mLb.clN.CollectMultipleMetrics.insert_size_histogram.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-NFYB3_R2.mLb.clN.CollectMultipleMetrics.insert_size_histogram.pdf
./bwa/mergedLibrary/picard_metrics/pdf/MYB59-3xHA_R1.mLb.clN.CollectMultipleMetrics.insert_size_histogram.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA_R2.mLb.clN.CollectMultipleMetrics.insert_size_histogram.pdf
./bwa/mergedLibrary/picard_metrics/pdf/NFYB3-3xHA_R3.mLb.clN.CollectMultipleMetrics.quality_distribution.pdf
./bwa/mergedLibrary/picard_metrics/pdf/NFYB3-3xHA_R3.mLb.clN.CollectMultipleMetrics.insert_size_histogram.pdf
./bwa/mergedLibrary/picard_metrics/pdf/NFYB3-3xHA_R3.mLb.clN.CollectMultipleMetrics.base_distribution_by_cycle.pdf
./bwa/mergedLibrary/picard_metrics/pdf/3xHA-NFYB3_R1.mLb.clN.CollectMultipleMetrics.base_distribution_by_cycle.pdf

Deeptools

Sequence coverage calculations

Publications

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086134/

Tutorials

https://deeptools.readthedocs.io/en/develop/

Plots heatmap (due to low coverage, didn't work well)

./bwa/mergedLibrary/deepTools/plotProfile/3xHA-NFYB3_R1.plotProfile.pdf
./bwa/mergedLibrary/deepTools/plotProfile/3xHA_R3.plotHeatmap.pdf
./bwa/mergedLibrary/deepTools/plotProfile/3xHA-MYB59_R1.plotProfile.pdf
./bwa/mergedLibrary/deepTools/plotProfile/HD-like-3xHA_R3.plotHeatmap.pdf
./bwa/mergedLibrary/deepTools/plotProfile/3xHA-HD-like_R3.plotProfile.pdf
./bwa/mergedLibrary/deepTools/plotProfile/HD-like-3xHA_R2.plotProfile.pdf
./bwa/mergedLibrary/deepTools/plotProfile/HD-like-3xHA_R3.plotProfile.pdf
./bwa/mergedLibrary/deepTools/plotProfile/3xHA_R1.plotProfile.pdf
./bwa/mergedLibrary/deepTools/plotProfile/MYB59-3xHA_R2.plotProfile.pdf
./bwa/mergedLibrary/deepTools/plotProfile/3xHA-MYB59_R3.plotProfile.pdf
./bwa/mergedLibrary/deepTools/plotProfile/MYB59-3xHA_R3.plotHeatmap.pdf
./bwa/mergedLibrary/deepTools/plotProfile/3xHA-MYB59_R2.plotHeatmap.pdf
./bwa/mergedLibrary/deepTools/plotProfile/NFYB3-3xHA_R1.plotProfile.pdf
./bwa/mergedLibrary/deepTools/plotProfile/MYB59-3xHA_R2.plotHeatmap.pdf
./bwa/mergedLibrary/deepTools/plotProfile/NFYB3-3xHA_R3.plotProfile.pdf
./bwa/mergedLibrary/deepTools/plotProfile/HD-like-3xHA_R2.plotHeatmap.pdf
./bwa/mergedLibrary/deepTools/plotProfile/3xHA-HD-like_R3.plotHeatmap.pdf
./bwa/mergedLibrary/deepTools/plotProfile/HD-like-3xHA_R1.plotProfile.pdf
./bwa/mergedLibrary/deepTools/plotProfile/MYB59-3xHA_R3.plotProfile.pdf
./bwa/mergedLibrary/deepTools/plotProfile/NFYB3-3xHA_R3.plotHeatmap.pdf
./bwa/mergedLibrary/deepTools/plotProfile/MYB59-3xHA_R1.plotHeatmap.pdf
./bwa/mergedLibrary/deepTools/plotProfile/MYB59-3xHA_R1.plotProfile.pdf
./bwa/mergedLibrary/deepTools/plotProfile/3xHA-HD-like_R2.plotProfile.pdf
./bwa/mergedLibrary/deepTools/plotProfile/3xHA-NFYB3_R3.plotProfile.pdf
./bwa/mergedLibrary/deepTools/plotProfile/3xHA-NFYB3_R3.plotHeatmap.pdf
./bwa/mergedLibrary/deepTools/plotProfile/3xHA_R2.plotProfile.pdf
./bwa/mergedLibrary/deepTools/plotProfile/3xHA-HD-like_R2.plotHeatmap.pdf
./bwa/mergedLibrary/deepTools/plotProfile/NFYB3-3xHA_R2.plotProfile.pdf
./bwa/mergedLibrary/deepTools/plotProfile/3xHA_R3.plotProfile.pdf
./bwa/mergedLibrary/deepTools/plotProfile/3xHA-HD-like_R1.plotHeatmap.pdf
./bwa/mergedLibrary/deepTools/plotProfile/3xHA_R1.plotHeatmap.pdf
./bwa/mergedLibrary/deepTools/plotProfile/NFYB3-3xHA_R2.plotHeatmap.pdf
./bwa/mergedLibrary/deepTools/plotProfile/3xHA-HD-like_R1.plotProfile.pdf
./bwa/mergedLibrary/deepTools/plotProfile/NFYB3-3xHA_R1.plotHeatmap.pdf
./bwa/mergedLibrary/deepTools/plotProfile/3xHA-NFYB3_R2.plotHeatmap.pdf
./bwa/mergedLibrary/deepTools/plotProfile/3xHA-NFYB3_R2.plotProfile.pdf
./bwa/mergedLibrary/deepTools/plotProfile/3xHA-MYB59_R3.plotHeatmap.pdf
./bwa/mergedLibrary/deepTools/plotProfile/3xHA-MYB59_R2.plotProfile.pdf
./bwa/mergedLibrary/deepTools/plotProfile/3xHA-NFYB3_R1.plotHeatmap.pdf
./bwa/mergedLibrary/deepTools/plotProfile/HD-like-3xHA_R1.plotHeatmap.pdf
./bwa/mergedLibrary/deepTools/plotProfile/3xHA-MYB59_R1.plotHeatmap.pdf
./bwa/mergedLibrary/deepTools/plotProfile/3xHA_R2.plotHeatmap.pdf
./bwa/mergedLibrary/deepTools/plotFingerprint/HD-like-3xHA_R3.plotFingerprint.pdf
./bwa/mergedLibrary/deepTools/plotFingerprint/3xHA-MYB59_R1.plotFingerprint.pdf
./bwa/mergedLibrary/deepTools/plotFingerprint/MYB59-3xHA_R1.plotFingerprint.pdf
./bwa/mergedLibrary/deepTools/plotFingerprint/MYB59-3xHA_R3.plotFingerprint.pdf
./bwa/mergedLibrary/deepTools/plotFingerprint/3xHA-NFYB3_R3.plotFingerprint.pdf
./bwa/mergedLibrary/deepTools/plotFingerprint/HD-like-3xHA_R1.plotFingerprint.pdf
./bwa/mergedLibrary/deepTools/plotFingerprint/3xHA-HD-like_R1.plotFingerprint.pdf
./bwa/mergedLibrary/deepTools/plotFingerprint/MYB59-3xHA_R2.plotFingerprint.pdf
./bwa/mergedLibrary/deepTools/plotFingerprint/HD-like-3xHA_R2.plotFingerprint.pdf
./bwa/mergedLibrary/deepTools/plotFingerprint/NFYB3-3xHA_R2.plotFingerprint.pdf
./bwa/mergedLibrary/deepTools/plotFingerprint/3xHA-NFYB3_R2.plotFingerprint.pdf
./bwa/mergedLibrary/deepTools/plotFingerprint/3xHA-HD-like_R3.plotFingerprint.pdf
./bwa/mergedLibrary/deepTools/plotFingerprint/3xHA-MYB59_R2.plotFingerprint.pdf
./bwa/mergedLibrary/deepTools/plotFingerprint/NFYB3-3xHA_R3.plotFingerprint.pdf
./bwa/mergedLibrary/deepTools/plotFingerprint/3xHA-MYB59_R3.plotFingerprint.pdf
./bwa/mergedLibrary/deepTools/plotFingerprint/NFYB3-3xHA_R1.plotFingerprint.pdf
./bwa/mergedLibrary/deepTools/plotFingerprint/3xHA-NFYB3_R1.plotFingerprint.pdf
./bwa/mergedLibrary/deepTools/plotFingerprint/3xHA-HD-like_R2.plotFingerprint.pdf

MACS2

Peak identifications

Publications

https://genomebiology.biomedcentral.com/articles/10.1186/gb-2008-9-9-r137 https://www.nature.com/articles/nprot.2012.101

Tutorials

https://hbctraining.github.io/Intro-to-ChIPseq/lessons/05_peak_calling_macs.html

MACS QC plots

./bwa/mergedLibrary/macs/broadPeak/qc/macs_peak.plots.pdf
./bwa/mergedLibrary/macs/broadPeak/qc/macs_annotatePeaks.plots.pdf

MACS intersect plots

./bwa/mergedLibrary/macs/broadPeak/consensus/MYB59/MYB59.consensus_peaks.boolean.intersect.plot.pdf
./bwa/mergedLibrary/macs/broadPeak/consensus/HDlike/HDlike.consensus_peaks.boolean.intersect.plot.pdf
./bwa/mergedLibrary/macs/broadPeak/consensus/NFYB3/NFYB3.consensus_peaks.boolean.intersect.plot.pdf

Syntax	Example	Reference
# Header	Header	基本排版
- Unordered List	Unordered List
1. Ordered List	Ordered List
- [ ] Todo List	Todo List
> Blockquote	Blockquote
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H~2~O	H₂O
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==Marked text==	Marked text
[link text](https:// "title")	Link
![image alt](https:// "title")	Image
`Code`	`Code`	在筆記中貼入程式碼
```javascript var i = 0; ```	`var i = 0;`	在筆記中貼入程式碼
:smile:		Emoji list
{%youtube youtube_id %}	Externals
$L^aT_eX$	L^aT_eX
:::info This is a alert area. :::	This is a alert area.