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Report generated at 2021-10-10 15:50:34

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	171638734	186874232
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	170208061	183817074
Mapped(QC-failed)	0	0
% Mapped	99.1700	98.3600
Paired	171638734	186874232
Paired(QC-failed)	0	0
Read1	85819367	93437116
Read1(QC-failed)	0	0
Read2	85819367	93437116
Read2(QC-failed)	0	0
Properly Paired	168947759	181190078
Properly Paired(QC-failed)	0	0
% Properly Paired	98.4300	96.9600
With itself	169667937	182989360
With itself(QC-failed)	0	0
Singletons	540124	827714
Singletons(QC-failed)	0	0
% Singleton	0.3100	0.4400
Diff. Chroms	428131	1011019
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	76266716	79420006
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4466540	3323828
Paired Opt. Dupes	43034	42686
% Dupes/100	0.0586	0.0419

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	76266550	79383916
Distinct Read Pairs	71800019	76061755
One Read Pair	67528650	72820637
Two Read Pairs	4084430	3164810
NRF = Distinct/Total	0.9414	0.9582
PBC1 = OnePair/Distinct	0.9405	0.9574
PBC2 = OnePair/TwoPair	16.5332	23.0095

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	143600352	152192356
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	143600352	152192356
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	143600352	152192356
Paired(QC-failed)	0	0
Read1	71800176	76096178
Read1(QC-failed)	0	0
Read2	71800176	76096178
Read2(QC-failed)	0	0
Properly Paired	143600352	152192356
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	143600352	152192356
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	107345
Np	0
N optimal	107345
N conservative	107345
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.	210
Corr. Est. Fragment Len.	0.2075
Phantom Peak	50
Corr. Phantom Peak	0.2084
Argmin. Corr.	1500
Min. Corr.	0.2024
NSC	1.0254
RSC	0.8498

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	0.7307

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	0.1031
AUC	0.4966
CHANCE divergence	0.1828
Elbow Point	0.0000
JS Distance	0.8069
Synthetic AUC	0.4984
Synthetic Elbow Point	0.5074
Synthetic JS Distance	0.5930