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Report generated at 2020-06-05 19:40:05

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	89973554	92143016
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	85032392	82943830
Mapped(QC-failed)	0	0
% Mapped	94.5100	90.0200
Paired	89973554	92143016
Paired(QC-failed)	0	0
Read1	44986777	46071508
Read1(QC-failed)	0	0
Read2	44986777	46071508
Read2(QC-failed)	0	0
Properly Paired	84341920	75643794
Properly Paired(QC-failed)	0	0
% Properly Paired	93.7400	82.0900
With itself	84645287	81703578
With itself(QC-failed)	0	0
Singletons	387105	1240252
Singletons(QC-failed)	0	0
% Singleton	0.4300	1.3500
Diff. Chroms	68748	199484
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	37753389	33771535
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2084479	1015840
Paired Opt. Dupes	3784	11140
% Dupes/100	0.0552	0.0301

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	37741041	33756367
Distinct Read Pairs	35657296	32741033
One Read Pair	33675801	31771390
Two Read Pairs	1885227	934950
NRF = Distinct/Total	0.9448	0.9699
PBC1 = OnePair/Distinct	0.9444	0.9704
PBC2 = OnePair/TwoPair	17.8630	33.9819

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	71337820	65511390
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	71337820	65511390
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	71337820	65511390
Paired(QC-failed)	0	0
Read1	35668910	32755695
Read1(QC-failed)	0	0
Read2	35668910	32755695
Read2(QC-failed)	0	0
Properly Paired	71337820	65511390
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	71337820	65511390
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	53104
Np	0
N optimal	53104
N conservative	53104
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.	170
Corr. Est. Fragment Len.	0.1819
Phantom Peak	50
Corr. Phantom Peak	0.1880
Argmin. Corr.	1500
Min. Corr.	0.1712
NSC	1.0620
RSC	0.6344

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	0.1262

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	0.2863
AUC	0.4952
CHANCE divergence	0.1062
Elbow Point	0.0000
JS Distance	0.5970
Synthetic AUC	0.5057
Synthetic Elbow Point	0.1277
Synthetic JS Distance	0.2786