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Report generated at 2022-01-06 16:58:03

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	152798576	146003154
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	150029839	143950255
Mapped(QC-failed)	0	0
% Mapped	98.1900	98.5900
Paired	152798576	146003154
Paired(QC-failed)	0	0
Read1	76399288	73001577
Read1(QC-failed)	0	0
Read2	76399288	73001577
Read2(QC-failed)	0	0
Properly Paired	148124182	139355986
Properly Paired(QC-failed)	0	0
% Properly Paired	96.9400	95.4500
With itself	149045092	143134940
With itself(QC-failed)	0	0
Singletons	984747	815315
Singletons(QC-failed)	0	0
% Singleton	0.6400	0.5600
Diff. Chroms	169207	200467
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	63267373	61294235
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	787551	434896
Paired Opt. Dupes	5110	3707
% Dupes/100	0.0124	0.0071

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	63082998	61180783
Distinct Read Pairs	62349318	60780225
One Read Pair	61635079	60396899
Two Read Pairs	703350	377062
NRF = Distinct/Total	0.9884	0.9935
PBC1 = OnePair/Distinct	0.9885	0.9937
PBC2 = OnePair/TwoPair	87.6307	160.1776

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	124959644	121718678
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	124959644	121718678
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	124959644	121718678
Paired(QC-failed)	0	0
Read1	62479822	60859339
Read1(QC-failed)	0	0
Read2	62479822	60859339
Read2(QC-failed)	0	0
Properly Paired	124959644	121718678
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	124959644	121718678
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	40898
Np	0
N optimal	40898
N conservative	40898
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.	0.1758
Phantom Peak	50
Corr. Phantom Peak	0.1869
Argmin. Corr.	1500
Min. Corr.	0.1705
NSC	1.0312
RSC	0.3250

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	0.0295

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	0.3412
AUC	0.4964
CHANCE divergence	0.0961
Elbow Point	0.0000
JS Distance	0.5068
Synthetic AUC	0.4977
Synthetic Elbow Point	0.0319
Synthetic JS Distance	0.1858