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Report generated at 2019-10-25 19:22:19

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	129137938	164317158
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	125900955	162006082
Mapped(QC-failed)	0	0
% Mapped	97.4900	98.5900
Paired	129137938	164317158
Paired(QC-failed)	0	0
Read1	64568969	82158579
Read1(QC-failed)	0	0
Read2	64568969	82158579
Read2(QC-failed)	0	0
Properly Paired	123401831	158686405
Properly Paired(QC-failed)	0	0
% Properly Paired	95.5600	96.5700
With itself	125066502	161193128
With itself(QC-failed)	0	0
Singletons	834453	812954
Singletons(QC-failed)	0	0
% Singleton	0.6500	0.4900
Diff. Chroms	1027024	1201289
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	51954573	66502967
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1666188	1918147
Paired Opt. Dupes	20921	14289
% Dupes/100	0.0321	0.0288

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	51954259	66493940
Distinct Read Pairs	50288085	64576078
One Read Pair	48665808	62704334
Two Read Pairs	1579473	1827454
NRF = Distinct/Total	0.9679	0.9712
PBC1 = OnePair/Distinct	0.9677	0.9710
PBC2 = OnePair/TwoPair	30.8114	34.3124

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	100576770	129169640
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	100576770	129169640
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	100576770	129169640
Paired(QC-failed)	0	0
Read1	50288385	64584820
Read1(QC-failed)	0	0
Read2	50288385	64584820
Read2(QC-failed)	0	0
Properly Paired	100576770	129169640
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	100576770	129169640
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	137195
Np	0
N optimal	137195
N conservative	137195
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.	0.1859
Phantom Peak	50
Corr. Phantom Peak	0.1937
Argmin. Corr.	1500
Min. Corr.	0.1812
NSC	1.0259
RSC	0.3764

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	0.2336

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	0.2392
AUC	0.4952
CHANCE divergence	0.1213
Elbow Point	0.0000
JS Distance	0.6241
Synthetic AUC	0.5033
Synthetic Elbow Point	0.2074
Synthetic JS Distance	0.3426