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Report generated at 2020-12-03 20:10:26

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	49204736	148269018
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	48400905	143500908
Mapped(QC-failed)	0	0
% Mapped	98.3700	96.7800
Paired	49204736	148269018
Paired(QC-failed)	0	0
Read1	24602368	74134509
Read1(QC-failed)	0	0
Read2	24602368	74134509
Read2(QC-failed)	0	0
Properly Paired	47826969	140225987
Properly Paired(QC-failed)	0	0
% Properly Paired	97.2000	94.5800
With itself	48184125	141622671
With itself(QC-failed)	0	0
Singletons	216780	1878237
Singletons(QC-failed)	0	0
% Singleton	0.4400	1.2700
Diff. Chroms	190336	652729
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	21190433	59090669
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	171717	523701
Paired Opt. Dupes	1992	14446
% Dupes/100	0.0081	0.0089

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	21187590	57674075
Distinct Read Pairs	21015896	57472830
One Read Pair	20845471	57272993
Two Read Pairs	169171	198503
NRF = Distinct/Total	0.9919	0.9965
PBC1 = OnePair/Distinct	0.9919	0.9965
PBC2 = OnePair/TwoPair	123.2213	288.5246

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	42037432	117133936
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	42037432	117133936
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	42037432	117133936
Paired(QC-failed)	0	0
Read1	21018716	58566968
Read1(QC-failed)	0	0
Read2	21018716	58566968
Read2(QC-failed)	0	0
Properly Paired	42037432	117133936
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	42037432	117133936
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	72402
Np	0
N optimal	72402
N conservative	72402
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.	195
Corr. Est. Fragment Len.	0.1965
Phantom Peak	50
Corr. Phantom Peak	0.2025
Argmin. Corr.	1500
Min. Corr.	0.1788
NSC	1.0986
RSC	0.7462

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	0.2015

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	0.2174
AUC	0.4937
CHANCE divergence	0.1720
Elbow Point	0.0000
JS Distance	0.6443
Synthetic AUC	0.5111
Synthetic Elbow Point	0.2521
Synthetic JS Distance	0.3592