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Report generated at 2019-10-31 04:50:20

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	100782274	244693048
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	99776940	242271295
Mapped(QC-failed)	0	0
% Mapped	99.0000	99.0100
Paired	100782274	244693048
Paired(QC-failed)	0	0
Read1	50391137	122346524
Read1(QC-failed)	0	0
Read2	50391137	122346524
Read2(QC-failed)	0	0
Properly Paired	98428945	235440196
Properly Paired(QC-failed)	0	0
% Properly Paired	97.6600	96.2200
With itself	99331135	241031519
With itself(QC-failed)	0	0
Singletons	445805	1239776
Singletons(QC-failed)	0	0
% Singleton	0.4400	0.5100
Diff. Chroms	578055	3646276
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	43113778	97950917
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	859468	2549032
Paired Opt. Dupes	9496	15998
% Dupes/100	0.0199	0.0260

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	43112432	97923980
Distinct Read Pairs	42252983	95375778
One Read Pair	41406844	92885043
Two Read Pairs	833021	2436078
NRF = Distinct/Total	0.9801	0.9740
PBC1 = OnePair/Distinct	0.9800	0.9739
PBC2 = OnePair/TwoPair	49.7068	38.1289

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	84508620	190803770
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	84508620	190803770
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	84508620	190803770
Paired(QC-failed)	0	0
Read1	42254310	95401885
Read1(QC-failed)	0	0
Read2	42254310	95401885
Read2(QC-failed)	0	0
Properly Paired	84508620	190803770
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	84508620	190803770
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	32839
Np	0
N optimal	32839
N conservative	32839
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.	220
Corr. Est. Fragment Len.	0.3238
Phantom Peak	55
Corr. Phantom Peak	0.3024
Argmin. Corr.	1500
Min. Corr.	0.1840
NSC	1.7594
RSC	1.1813

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	0.4490

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	0.1820
AUC	0.4946
CHANCE divergence	0.1184
Elbow Point	0.0000
JS Distance	0.8758
Synthetic AUC	0.5080
Synthetic Elbow Point	0.4523
Synthetic JS Distance	0.5035