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Report generated at 2019-11-03 14:43:03

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	132566572	175026970
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	130762063	171819448
Mapped(QC-failed)	0	0
% Mapped	98.6400	98.1700
Paired	132566572	175026970
Paired(QC-failed)	0	0
Read1	66283286	87513485
Read1(QC-failed)	0	0
Read2	66283286	87513485
Read2(QC-failed)	0	0
Properly Paired	129277770	168294620
Properly Paired(QC-failed)	0	0
% Properly Paired	97.5200	96.1500
With itself	130270440	170965028
With itself(QC-failed)	0	0
Singletons	491623	854420
Singletons(QC-failed)	0	0
% Singleton	0.3700	0.4900
Diff. Chroms	211349	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	59136695	74970360
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2023141	1349605
Paired Opt. Dupes	14707	20203
% Dupes/100	0.0342	0.0180

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	59118582	74828889
Distinct Read Pairs	57096135	73485563
One Read Pair	55121924	72156748
Two Read Pairs	1927163	1315961
NRF = Distinct/Total	0.9658	0.9820
PBC1 = OnePair/Distinct	0.9654	0.9819
PBC2 = OnePair/TwoPair	28.6026	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	114227108	147241510
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	114227108	147241510
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	114227108	147241510
Paired(QC-failed)	0	0
Read1	57113554	73620755
Read1(QC-failed)	0	0
Read2	57113554	73620755
Read2(QC-failed)	0	0
Properly Paired	114227108	147241510
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	114227108	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	72480
Np	0
N optimal	72480
N conservative	72480
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.	180
Corr. Est. Fragment Len.	0.2023
Phantom Peak	50
Corr. Phantom Peak	0.2044
Argmin. Corr.	1500
Min. Corr.	0.1854
NSC	1.0911
RSC	0.8883

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	0.3259

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	0.2356
AUC	0.4962
CHANCE divergence	0.0982
Elbow Point	0.0000
JS Distance	0.7472
Synthetic AUC	0.5061
Synthetic Elbow Point	0.2956
Synthetic JS Distance	0.3825