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Report generated at 2021-06-17 08:45:34

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	56164324	63584528
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	54868097	62609767
Mapped(QC-failed)	0	0
% Mapped	97.6900	98.4700
Paired	56164324	63584528
Paired(QC-failed)	0	0
Read1	28082162	31792264
Read1(QC-failed)	0	0
Read2	28082162	31792264
Read2(QC-failed)	0	0
Properly Paired	54458025	59075555
Properly Paired(QC-failed)	0	0
% Properly Paired	96.9600	92.9100
With itself	54622683	62240288
With itself(QC-failed)	0	0
Singletons	245414	369479
Singletons(QC-failed)	0	0
% Singleton	0.4400	0.5800
Diff. Chroms	23602	177999
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	24657839	25685208
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	956941	129982
Paired Opt. Dupes	43911	62665
% Dupes/100	0.0388	0.0051

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	24656541	25684816
Distinct Read Pairs	23699646	25554835
One Read Pair	22837819	25428261
Two Read Pairs	797657	124921
NRF = Distinct/Total	0.9612	0.9949
PBC1 = OnePair/Distinct	0.9636	0.9950
PBC2 = OnePair/TwoPair	28.6311	203.5547

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	47401796	51110452
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	47401796	51110452
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	47401796	51110452
Paired(QC-failed)	0	0
Read1	23700898	25555226
Read1(QC-failed)	0	0
Read2	23700898	25555226
Read2(QC-failed)	0	0
Properly Paired	47401796	51110452
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	47401796	51110452
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	104610
Np	0
N optimal	104610
N conservative	104610
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.	150
Corr. Est. Fragment Len.	0.2589
Phantom Peak	55
Corr. Phantom Peak	0.1809
Argmin. Corr.	1500
Min. Corr.	0.1517
NSC	1.7073
RSC	3.6694

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	0.4523

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	0.1583
AUC	0.4939
CHANCE divergence	0.1651
Elbow Point	0.0000
JS Distance	0.8083
Synthetic AUC	0.4959
Synthetic Elbow Point	0.3754
Synthetic JS Distance	0.4917