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Report generated at 2020-06-05 23:36:25

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	146496114	70427534
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	141821685	69036339
Mapped(QC-failed)	0	0
% Mapped	96.8100	98.0200
Paired	146496114	70427534
Paired(QC-failed)	0	0
Read1	73248057	35213767
Read1(QC-failed)	0	0
Read2	73248057	35213767
Read2(QC-failed)	0	0
Properly Paired	139722120	68456819
Properly Paired(QC-failed)	0	0
% Properly Paired	95.3800	97.2000
With itself	140689241	68728851
With itself(QC-failed)	0	0
Singletons	1132444	307488
Singletons(QC-failed)	0	0
% Singleton	0.7700	0.4400
Diff. Chroms	135869	67600
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	54092006	30027198
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	15194829	502248
Paired Opt. Dupes	10489	5515
% Dupes/100	0.2809	0.0167

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	54082702	29867173
Distinct Read Pairs	38890540	29376484
One Read Pair	27380785	28892611
Two Read Pairs	8613450	477189
NRF = Distinct/Total	0.7191	0.9836
PBC1 = OnePair/Distinct	0.7040	0.9835
PBC2 = OnePair/TwoPair	3.1788	60.5475

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	77794354	59049900
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	77794354	59049900
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	77794354	59049900
Paired(QC-failed)	0	0
Read1	38897177	29524950
Read1(QC-failed)	0	0
Read2	38897177	29524950
Read2(QC-failed)	0	0
Properly Paired	77794354	59049900
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	77794354	59049900
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	154153
Np	0
N optimal	154153
N conservative	154153
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.	205
Corr. Est. Fragment Len.	0.1846
Phantom Peak	50
Corr. Phantom Peak	0.2153
Argmin. Corr.	1500
Min. Corr.	0.1748
NSC	1.0566
RSC	0.2438

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	0.1956

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	0.2402
AUC	0.4954
CHANCE divergence	0.1276
Elbow Point	0.0000
JS Distance	0.6228
Synthetic AUC	0.5035
Synthetic Elbow Point	0.1629
Synthetic JS Distance	0.3361