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Report generated at 2021-03-18 10:09:43

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	46831350	107748822
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	46233748	105210529
Mapped(QC-failed)	0	0
% Mapped	98.7200	97.6400
Paired	46831350	107748822
Paired(QC-failed)	0	0
Read1	23415675	53874411
Read1(QC-failed)	0	0
Read2	23415675	53874411
Read2(QC-failed)	0	0
Properly Paired	42302010	89353817
Properly Paired(QC-failed)	0	0
% Properly Paired	90.3300	82.9300
With itself	45975503	104162194
With itself(QC-failed)	0	0
Singletons	258245	1048335
Singletons(QC-failed)	0	0
% Singleton	0.5500	0.9700
Diff. Chroms	2989469	11301530
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	19750231	39900791
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	585845	469856
Paired Opt. Dupes	1636	1823
% Dupes/100	0.0297	0.0118

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	19740480	39896493
Distinct Read Pairs	19155235	39426880
One Read Pair	18669364	38982156
Two Read Pairs	423827	431298
NRF = Distinct/Total	0.9704	0.9882
PBC1 = OnePair/Distinct	0.9746	0.9887
PBC2 = OnePair/TwoPair	44.0495	90.3833

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	38328772	78861870
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	38328772	78861870
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	38328772	78861870
Paired(QC-failed)	0	0
Read1	19164386	39430935
Read1(QC-failed)	0	0
Read2	19164386	39430935
Read2(QC-failed)	0	0
Properly Paired	38328772	78861870
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	38328772	78861870
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	94621
Np	0
N optimal	94621
N conservative	94621
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.	160
Corr. Est. Fragment Len.	0.2681
Phantom Peak	55
Corr. Phantom Peak	0.2130
Argmin. Corr.	1500
Min. Corr.	0.1638
NSC	1.6363
RSC	2.1190

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	0.6263

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	0.0843
AUC	0.4934
CHANCE divergence	0.3558
Elbow Point	0.0000
JS Distance	0.8587
Synthetic AUC	0.4978
Synthetic Elbow Point	0.4935
Synthetic JS Distance	0.5894