# ChIP-Seq Pipeline summary
1. Raw read QC (FastQC)
2. Adapter trimming (Trim Galore!)
3. Alignment (BWA)
4. Mark duplicates (picard)
5. 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)
6. Alignment-level QC and estimation of library complexity (picard, Preseq)\
7. Create normalised bigWig files scaled to 1 million mapped reads (BEDTools, bedGraphToBigWig)
8. Generate gene-body meta-profile from bigWig files (deepTools)
9. Calculate genome-wide IP enrichment relative to control (deepTools)
10. Calculate strand cross-correlation peak and ChIP-seq quality measures including NSC and RSC (phantompeakqualtools)
11. 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