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Report generated at 2021-02-05 10:19:09

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	51852338	99127026
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	50956321	97503736
Mapped(QC-failed)	0	0
% Mapped	98.2700	98.3600
Paired	51852338	99127026
Paired(QC-failed)	0	0
Read1	25926169	49563513
Read1(QC-failed)	0	0
Read2	25926169	49563513
Read2(QC-failed)	0	0
Properly Paired	50620126	95250672
Properly Paired(QC-failed)	0	0
% Properly Paired	97.6200	96.0900
With itself	50702541	96906871
With itself(QC-failed)	0	0
Singletons	253780	596865
Singletons(QC-failed)	0	0
% Singleton	0.4900	0.6000
Diff. Chroms	10611	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	23783405	41226719
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1566144	286989
Paired Opt. Dupes	2858	26725
% Dupes/100	0.0659	0.0070

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	23775289	41202948
Distinct Read Pairs	22209538	40918073
One Read Pair	20889885	40653897
Two Read Pairs	1173897	257278
NRF = Distinct/Total	0.9341	0.9931
PBC1 = OnePair/Distinct	0.9406	0.9935
PBC2 = OnePair/TwoPair	17.7953	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	44434522	81879460
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	44434522	81879460
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	44434522	81879460
Paired(QC-failed)	0	0
Read1	22217261	40939730
Read1(QC-failed)	0	0
Read2	22217261	40939730
Read2(QC-failed)	0	0
Properly Paired	44434522	81879460
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	44434522	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	91575
Np	0
N optimal	91575
N conservative	91575
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.	0.3566
Phantom Peak	55
Corr. Phantom Peak	0.2511
Argmin. Corr.	1500
Min. Corr.	0.1472
NSC	2.4229
RSC	2.0149

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	0.7350

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	0.0500
AUC	0.4937
CHANCE divergence	0.4623
Elbow Point	0.0000
JS Distance	0.9017
Synthetic AUC	0.5028
Synthetic Elbow Point	0.5619
Synthetic JS Distance	0.6675