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Report generated at 2022-01-08 00:33:18

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	108885584	130176754
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	107622302	124658283
Mapped(QC-failed)	0	0
% Mapped	98.8400	95.7600
Paired	108885584	130176754
Paired(QC-failed)	0	0
Read1	54442792	65088377
Read1(QC-failed)	0	0
Read2	54442792	65088377
Read2(QC-failed)	0	0
Properly Paired	92049700	102167555
Properly Paired(QC-failed)	0	0
% Properly Paired	84.5400	78.4800
With itself	106786852	122523087
With itself(QC-failed)	0	0
Singletons	835450	2135196
Singletons(QC-failed)	0	0
% Singleton	0.7700	1.6400
Diff. Chroms	11726912	14641335
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	42904340	44771849
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	608665	568051
Paired Opt. Dupes	1354	648
% Dupes/100	0.0142	0.0127

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	42862898	44746969
Distinct Read Pairs	42260950	44182877
One Read Pair	41682347	43638722
Two Read Pairs	557427	533088
NRF = Distinct/Total	0.9860	0.9874
PBC1 = OnePair/Distinct	0.9863	0.9877
PBC2 = OnePair/TwoPair	74.7763	81.8603

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	84591350	88407596
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	84591350	88407596
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	84591350	88407596
Paired(QC-failed)	0	0
Read1	42295675	44203798
Read1(QC-failed)	0	0
Read2	42295675	44203798
Read2(QC-failed)	0	0
Properly Paired	84591350	88407596
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	84591350	88407596
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	223571
Np	0
N optimal	223571
N conservative	223571
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.	125
Corr. Est. Fragment Len.	0.1919
Phantom Peak	55
Corr. Phantom Peak	0.1867
Argmin. Corr.	1500
Min. Corr.	0.1841
NSC	1.0423
RSC	2.9413

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	0.5864

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	0.1267
AUC	0.4956
CHANCE divergence	0.2437
Elbow Point	0.0000
JS Distance	0.7644
Synthetic AUC	0.5072
Synthetic Elbow Point	0.3767
Synthetic JS Distance	0.5119