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Report generated at 2020-05-18 19:04:03

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	88571282	188531594
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	84333999	183497192
Mapped(QC-failed)	0	0
% Mapped	95.2200	97.3300
Paired	88571282	188531594
Paired(QC-failed)	0	0
Read1	44285641	94265797
Read1(QC-failed)	0	0
Read2	44285641	94265797
Read2(QC-failed)	0	0
Properly Paired	82885369	180692140
Properly Paired(QC-failed)	0	0
% Properly Paired	93.5800	95.8400
With itself	83864850	182539954
With itself(QC-failed)	0	0
Singletons	469149	957238
Singletons(QC-failed)	0	0
% Singleton	0.5300	0.5100
Diff. Chroms	589027	942066
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	36546899	78941456
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	183303	448927
Paired Opt. Dupes	1772	2929
% Dupes/100	0.0050	0.0057

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	36542821	78883545
Distinct Read Pairs	36359538	78435677
One Read Pair	36177188	77991934
Two Read Pairs	181426	439949
NRF = Distinct/Total	0.9950	0.9943
PBC1 = OnePair/Distinct	0.9950	0.9943
PBC2 = OnePair/TwoPair	199.4047	177.2749

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	72727192	156985058
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	72727192	156985058
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	72727192	156985058
Paired(QC-failed)	0	0
Read1	36363596	78492529
Read1(QC-failed)	0	0
Read2	36363596	78492529
Read2(QC-failed)	0	0
Properly Paired	72727192	156985058
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	72727192	156985058
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	175662
Np	0
N optimal	175662
N conservative	175662
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.	135
Corr. Est. Fragment Len.	0.1892
Phantom Peak	50
Corr. Phantom Peak	0.2029
Argmin. Corr.	1500
Min. Corr.	0.1813
NSC	1.0436
RSC	0.3661

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	0.2915

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	0.2209
AUC	0.4952
CHANCE divergence	0.1175
Elbow Point	0.0000
JS Distance	0.6995
Synthetic AUC	0.5044
Synthetic Elbow Point	0.2127
Synthetic JS Distance	0.3742