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Report generated at 2021-10-09 22:40:04

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	106157766	202350424
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	100857897	198649849
Mapped(QC-failed)	0	0
% Mapped	95.0100	98.1700
Paired	106157766	202350424
Paired(QC-failed)	0	0
Read1	53078883	101175212
Read1(QC-failed)	0	0
Read2	53078883	101175212
Read2(QC-failed)	0	0
Properly Paired	99233336	191032553
Properly Paired(QC-failed)	0	0
% Properly Paired	93.4800	94.4100
With itself	100119453	196787032
With itself(QC-failed)	0	0
Singletons	738444	1862817
Singletons(QC-failed)	0	0
% Singleton	0.7000	0.9200
Diff. Chroms	545369	4083046
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	43510173	79868417
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	5551101	3252613
Paired Opt. Dupes	23261	36998
% Dupes/100	0.1276	0.0407

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	43507025	79802498
Distinct Read Pairs	37956312	76553268
One Read Pair	33002412	73415319
Two Read Pairs	4413355	3032014
NRF = Distinct/Total	0.8724	0.9593
PBC1 = OnePair/Distinct	0.8695	0.9590
PBC2 = OnePair/TwoPair	7.4779	24.2134

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	75918144	153231608
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	75918144	153231608
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	75918144	153231608
Paired(QC-failed)	0	0
Read1	37959072	76615804
Read1(QC-failed)	0	0
Read2	37959072	76615804
Read2(QC-failed)	0	0
Properly Paired	75918144	153231608
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	75918144	153231608
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	99853
Np	0
N optimal	99853
N conservative	99853
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.	200
Corr. Est. Fragment Len.	0.2139
Phantom Peak	50
Corr. Phantom Peak	0.2112
Argmin. Corr.	1500
Min. Corr.	0.1840
NSC	1.1627
RSC	1.1002

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	0.4566

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	0.1718
AUC	0.4943
CHANCE divergence	0.1293
Elbow Point	0.0000
JS Distance	0.8042
Synthetic AUC	0.5043
Synthetic Elbow Point	0.3881
Synthetic JS Distance	0.4707