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Report generated at 2021-02-05 21:39:58

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	132186108	100610396
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	130830886	98910281
Mapped(QC-failed)	0	0
% Mapped	98.9700	98.3100
Paired	132186108	100610396
Paired(QC-failed)	0	0
Read1	66093054	50305198
Read1(QC-failed)	0	0
Read2	66093054	50305198
Read2(QC-failed)	0	0
Properly Paired	127237238	96866538
Properly Paired(QC-failed)	0	0
% Properly Paired	96.2600	96.2800
With itself	130183038	98283644
With itself(QC-failed)	0	0
Singletons	647848	626637
Singletons(QC-failed)	0	0
% Singleton	0.4900	0.6200
Diff. Chroms	122735	146099
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	55730732	42057260
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	680492	223838
Paired Opt. Dupes	18535	11806
% Dupes/100	0.0122	0.0053

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	55650537	42020997
Distinct Read Pairs	54980486	41800825
One Read Pair	54321267	41591190
Two Read Pairs	649718	205559
NRF = Distinct/Total	0.9880	0.9948
PBC1 = OnePair/Distinct	0.9880	0.9950
PBC2 = OnePair/TwoPair	83.6075	202.3321

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	110100480	83666844
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	110100480	83666844
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	110100480	83666844
Paired(QC-failed)	0	0
Read1	55050240	41833422
Read1(QC-failed)	0	0
Read2	55050240	41833422
Read2(QC-failed)	0	0
Properly Paired	110100480	83666844
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	110100480	83666844
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	204078
Np	0
N optimal	204078
N conservative	204078
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.	145
Corr. Est. Fragment Len.	0.1818
Phantom Peak	50
Corr. Phantom Peak	0.1829
Argmin. Corr.	1500
Min. Corr.	0.1754
NSC	1.0365
RSC	0.8534

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	0.1311

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	0.2533
AUC	0.4960
CHANCE divergence	0.1096
Elbow Point	0.0000
JS Distance	0.6025
Synthetic AUC	0.5063
Synthetic Elbow Point	0.1006
Synthetic JS Distance	0.3231