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Report generated at 2022-01-06 06:21:38

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	121983394	100267900
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	116615981	98810234
Mapped(QC-failed)	0	0
% Mapped	95.6000	98.5500
Paired	121983394	100267900
Paired(QC-failed)	0	0
Read1	60991697	50133950
Read1(QC-failed)	0	0
Read2	60991697	50133950
Read2(QC-failed)	0	0
Properly Paired	114297216	95001356
Properly Paired(QC-failed)	0	0
% Properly Paired	93.7000	94.7500
With itself	115262014	98214055
With itself(QC-failed)	0	0
Singletons	1353967	596179
Singletons(QC-failed)	0	0
% Singleton	1.1100	0.5900
Diff. Chroms	117644	104040
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	43643439	42286553
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1455782	313043
Paired Opt. Dupes	1408	1742
% Dupes/100	0.0334	0.0074

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	43633940	42271771
Distinct Read Pairs	42178730	41959879
One Read Pair	40866945	41660125
Two Read Pairs	1254576	294758
NRF = Distinct/Total	0.9667	0.9926
PBC1 = OnePair/Distinct	0.9689	0.9929
PBC2 = OnePair/TwoPair	32.5743	141.3367

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	84375314	83947020
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	84375314	83947020
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	84375314	83947020
Paired(QC-failed)	0	0
Read1	42187657	41973510
Read1(QC-failed)	0	0
Read2	42187657	41973510
Read2(QC-failed)	0	0
Properly Paired	84375314	83947020
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	84375314	83947020
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	154706
Np	0
N optimal	154706
N conservative	154706
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.	-10
Corr. Est. Fragment Len.	0.1931
Phantom Peak	50
Corr. Phantom Peak	0.2179
Argmin. Corr.	1500
Min. Corr.	0.1804
NSC	1.0703
RSC	0.3388

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	0.3310

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	0.1864
AUC	0.4956
CHANCE divergence	0.1918
Elbow Point	0.0000
JS Distance	0.6530
Synthetic AUC	0.5052
Synthetic Elbow Point	0.2638
Synthetic JS Distance	0.4105