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Report generated at 2021-10-10 04:36:56

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	71227230	202126234
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	53932750	198799328
Mapped(QC-failed)	0	0
% Mapped	75.7200	98.3500
Paired	71227230	202126234
Paired(QC-failed)	0	0
Read1	35613615	101063117
Read1(QC-failed)	0	0
Read2	35613615	101063117
Read2(QC-failed)	0	0
Properly Paired	52556887	176384044
Properly Paired(QC-failed)	0	0
% Properly Paired	73.7900	87.2600
With itself	53374327	196644255
With itself(QC-failed)	0	0
Singletons	558423	2155073
Singletons(QC-failed)	0	0
% Singleton	0.7800	1.0700
Diff. Chroms	143826	15415697
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	21344463	72658135
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	10033150	9622785
Paired Opt. Dupes	2646	11648
% Dupes/100	0.4701	0.1324

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	21339023	72505168
Distinct Read Pairs	11308359	62908922
One Read Pair	6359582	54529901
Two Read Pairs	2518980	7308755
NRF = Distinct/Total	0.5299	0.8676
PBC1 = OnePair/Distinct	0.5624	0.8668
PBC2 = OnePair/TwoPair	2.5247	7.4609

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	22622626	126070700
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	22622626	126070700
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	22622626	126070700
Paired(QC-failed)	0	0
Read1	11311313	63035350
Read1(QC-failed)	0	0
Read2	11311313	63035350
Read2(QC-failed)	0	0
Properly Paired	22622626	126070700
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	22622626	126070700
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	40581
Np	0
N optimal	40581
N conservative	40581
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.	0.1060
Phantom Peak	50
Corr. Phantom Peak	0.1171
Argmin. Corr.	1500
Min. Corr.	0.1002
NSC	1.0581
RSC	0.3448

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	0.0583

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	0.2429
AUC	0.4895
CHANCE divergence	0.2247
Elbow Point	0.0000
JS Distance	0.5608
Synthetic AUC	0.5126
Synthetic Elbow Point	0.1463
Synthetic JS Distance	0.2628