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Report generated at 2020-05-02 13:30:40

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	46017494	65266666
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	41543333	62068581
Mapped(QC-failed)	0	0
% Mapped	90.2800	95.1000
Paired	46017494	65266666
Paired(QC-failed)	0	0
Read1	23008747	32633333
Read1(QC-failed)	0	0
Read2	23008747	32633333
Read2(QC-failed)	0	0
Properly Paired	40239440	52881751
Properly Paired(QC-failed)	0	0
% Properly Paired	87.4400	81.0200
With itself	40868781	60433888
With itself(QC-failed)	0	0
Singletons	674552	1634693
Singletons(QC-failed)	0	0
% Singleton	1.4700	2.5000
Diff. Chroms	309520	5291648
Diff. Chroms (QC-failed)	0	0

Marking duplicates (filtered BAM)

Filtered out (samtools view -F 1804):

read unmapped (0x4)
mate unmapped (0x8)
not primary alignment (0x100)
read fails platform/vendor quality checks (0x200)
read is PCR or optical duplicate (0x400)

	rep1	ctl1
Unpaired Reads	0	0
Paired Reads	17433032	20779273
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	237462	269236
Paired Opt. Dupes	2970	2954
% Dupes/100	0.0136	0.0130

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	17432370	20779235
Distinct Read Pairs	17194914	20509999
One Read Pair	16960163	20243741
Two Read Pairs	232072	263299
NRF = Distinct/Total	0.9864	0.9870
PBC1 = OnePair/Distinct	0.9863	0.9870
PBC2 = OnePair/TwoPair	73.0815	76.8850

Mitochondrial reads are filtered out.

NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally

0-0.5 is severe bottlenecking
0.5-0.8 is moderate bottlenecking
0.8-0.9 is mild bottlenecking
0.9-1.0 is no bottlenecking

Flagstat (filtered/deduped BAM)

Filtered and duplicates removed

	rep1	ctl1
Total	34391140	41020074
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	34391140	41020074
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	34391140	41020074
Paired(QC-failed)	0	0
Read1	17195570	20510037
Read1(QC-failed)	0	0
Read2	17195570	20510037
Read2(QC-failed)	0	0
Properly Paired	34391140	41020074
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	34391140	41020074
With itself(QC-failed)	0	0
Singletons	0	0
Singletons(QC-failed)	0	0
% Singleton	0.0000	0.0000
Diff. Chroms	0	0
Diff. Chroms (QC-failed)	0	0

Peak calling

Reproducibility QC and peak detection statistics

The number of peaks is capped at 300K for peak-caller MACS2

	overlap
Nt	0
N1	135791
Np	0
N optimal	135791
N conservative	135791
Optimal Set	rep1-pr
Conservative Set	rep1-pr
Rescue Ratio	0.0000
Self Consistency Ratio	1.0000
Reproducibility	pass

Overlapping peaks

N1: Replicate 1 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Nt: True Replicate consisten overlapping peaks (comparing true replicates Rep1 vs Rep2 )
Np: Pooled-pseudoreplicate consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling pooled reads from Rep1 and Rep2 )
Self-consistency Ratio: max(N1,N2) / min (N1,N2)
Rescue Ratio: max(Np,Nt) / min (Np,Nt)
Reproducibility Test: If Self-consistency Ratio >2 AND Rescue Ratio > 2, then 'Fail' else 'Pass'

Enrichment

Strand cross-correlation measures

Performed on subsampled reads (15M)

	rep1
Reads	15000000
Est. Fragment Len.	270
Corr. Est. Fragment Len.	0.1946
Phantom Peak	50
Corr. Phantom Peak	0.1915
Argmin. Corr.	1500
Min. Corr.	0.1738
NSC	1.1197
RSC	1.1729

NOTE1: For SE datasets, reads from replicates are randomly subsampled.
NOTE2: For PE datasets, the first end of each read-pair is selected and the reads are then randomly subsampled.

Normalized strand cross-correlation coefficient (NSC) = col9 in outFile
Relative strand cross-correlation coefficient (RSC) = col10 in outFile
Estimated fragment length = col3 in outFile, take the top value

Fraction of reads in overlapping peaks

	rep1-pr
Fraction of Reads in Peak	0.1762

ppr: Overlapping peaks comparing pooled pseudo replicates
rep1-pr: Overlapping peaks comparing pseudoreplicates from replicate 1
rep2-pr: Overlapping peaks comparing pseudoreplicates from replicate 2
repi-repj: Overlapping peaks comparing true replicates (rep i vs. rep j)

Other quality metrics

Fingerprint and Jensen-Shannon distance

	rep1
% genome enriched	0.1529
AUC	0.4930
CHANCE divergence	0.4077
Elbow Point	0.0000
JS Distance	0.6622
Synthetic AUC	0.4960
Synthetic Elbow Point	0.0884
Synthetic JS Distance	0.3584