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Report generated at 2019-11-04 00:37:16

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	158759758	175026970
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	152234224	171819448
Mapped(QC-failed)	0	0
% Mapped	95.8900	98.1700
Paired	158759758	175026970
Paired(QC-failed)	0	0
Read1	79379879	87513485
Read1(QC-failed)	0	0
Read2	79379879	87513485
Read2(QC-failed)	0	0
Properly Paired	148136315	168294620
Properly Paired(QC-failed)	0	0
% Properly Paired	93.3100	96.1500
With itself	150656133	170965028
With itself(QC-failed)	0	0
Singletons	1578091	854420
Singletons(QC-failed)	0	0
% Singleton	0.9900	0.4900
Diff. Chroms	575763	1256632
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	54862035	74970360
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1214444	1349605
Paired Opt. Dupes	14763	20203
% Dupes/100	0.0221	0.0180

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	54859827	74828889
Distinct Read Pairs	53645429	73485563
One Read Pair	52472543	72156748
Two Read Pairs	1146516	1315961
NRF = Distinct/Total	0.9779	0.9820
PBC1 = OnePair/Distinct	0.9781	0.9819
PBC2 = OnePair/TwoPair	45.7670	54.8320

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	107295182	147241510
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	107295182	147241510
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	107295182	147241510
Paired(QC-failed)	0	0
Read1	53647591	73620755
Read1(QC-failed)	0	0
Read2	53647591	73620755
Read2(QC-failed)	0	0
Properly Paired	107295182	147241510
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	107295182	147241510
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	206516
Np	0
N optimal	206516
N conservative	206516
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.	120
Corr. Est. Fragment Len.	0.2102
Phantom Peak	50
Corr. Phantom Peak	0.2514
Argmin. Corr.	1500
Min. Corr.	0.2009
NSC	1.0459
RSC	0.1827

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	0.4240

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	0.1776
AUC	0.4961
CHANCE divergence	0.1652
Elbow Point	0.0000
JS Distance	0.6885
Synthetic AUC	0.4984
Synthetic Elbow Point	0.3227
Synthetic JS Distance	0.4404