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Report generated at 2021-10-23 03:45:51

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	88941786	219992592
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	86115094	213659622
Mapped(QC-failed)	0	0
% Mapped	96.8200	97.1200
Paired	88941786	219992592
Paired(QC-failed)	0	0
Read1	44470893	109996296
Read1(QC-failed)	0	0
Read2	44470893	109996296
Read2(QC-failed)	0	0
Properly Paired	84333529	197087249
Properly Paired(QC-failed)	0	0
% Properly Paired	94.8200	89.5900
With itself	85385713	211480826
With itself(QC-failed)	0	0
Singletons	729381	2178796
Singletons(QC-failed)	0	0
% Singleton	0.8200	0.9900
Diff. Chroms	371880	10437284
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	35310717	82195568
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	10356993	8102886
Paired Opt. Dupes	7396	12260
% Dupes/100	0.2933	0.0986

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	35304947	82007813
Distinct Read Pairs	24949433	73933688
One Read Pair	17431404	66591320
Two Read Pairs	5387089	6676828
NRF = Distinct/Total	0.7067	0.9015
PBC1 = OnePair/Distinct	0.6987	0.9007
PBC2 = OnePair/TwoPair	3.2358	9.9735

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	49907448	148185364
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	49907448	148185364
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	49907448	148185364
Paired(QC-failed)	0	0
Read1	24953724	74092682
Read1(QC-failed)	0	0
Read2	24953724	74092682
Read2(QC-failed)	0	0
Properly Paired	49907448	148185364
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	49907448	148185364
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	72810
Np	0
N optimal	72810
N conservative	72810
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.	165
Corr. Est. Fragment Len.	0.1648
Phantom Peak	50
Corr. Phantom Peak	0.1668
Argmin. Corr.	1500
Min. Corr.	0.1534
NSC	1.0743
RSC	0.8507

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	0.1333

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	0.2653
AUC	0.4929
CHANCE divergence	0.1275
Elbow Point	0.0000
JS Distance	0.5952
Synthetic AUC	0.4949
Synthetic Elbow Point	0.1834
Synthetic JS Distance	0.2933