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Report generated at 2021-02-05 14:01:51

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	98837878	99127026
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	97880529	97503736
Mapped(QC-failed)	0	0
% Mapped	99.0300	98.3600
Paired	98837878	99127026
Paired(QC-failed)	0	0
Read1	49418939	49563513
Read1(QC-failed)	0	0
Read2	49418939	49563513
Read2(QC-failed)	0	0
Properly Paired	89907734	95250672
Properly Paired(QC-failed)	0	0
% Properly Paired	90.9600	96.0900
With itself	97379557	96906871
With itself(QC-failed)	0	0
Singletons	500972	596865
Singletons(QC-failed)	0	0
% Singleton	0.5100	0.6000
Diff. Chroms	183561	136587
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	39545896	41226719
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	522273	286989
Paired Opt. Dupes	6022	26725
% Dupes/100	0.0132	0.0070

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	39510800	41202948
Distinct Read Pairs	38991094	40918073
One Read Pair	38480060	40653897
Two Read Pairs	503159	257278
NRF = Distinct/Total	0.9868	0.9931
PBC1 = OnePair/Distinct	0.9869	0.9935
PBC2 = OnePair/TwoPair	76.4769	158.0154

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	78047246	81879460
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	78047246	81879460
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	78047246	81879460
Paired(QC-failed)	0	0
Read1	39023623	40939730
Read1(QC-failed)	0	0
Read2	39023623	40939730
Read2(QC-failed)	0	0
Properly Paired	78047246	81879460
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	78047246	81879460
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	203283
Np	0
N optimal	203283
N conservative	203283
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.	0.1867
Phantom Peak	45
Corr. Phantom Peak	0.1851
Argmin. Corr.	1500
Min. Corr.	0.1781
NSC	1.0486
RSC	1.2388

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	0.1832

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	0.2212
AUC	0.4952
CHANCE divergence	0.1629
Elbow Point	0.0000
JS Distance	0.6191
Synthetic AUC	0.4989
Synthetic Elbow Point	0.1324
Synthetic JS Distance	0.3544