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Report generated at 2020-05-13 21:45:50

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	40918794	42861406
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	39792303	41140907
Mapped(QC-failed)	0	0
% Mapped	97.2500	95.9900
Paired	40918794	42861406
Paired(QC-failed)	0	0
Read1	20459397	21430703
Read1(QC-failed)	0	0
Read2	20459397	21430703
Read2(QC-failed)	0	0
Properly Paired	38236365	38139893
Properly Paired(QC-failed)	0	0
% Properly Paired	93.4400	88.9800
With itself	39003095	39997010
With itself(QC-failed)	0	0
Singletons	789208	1143897
Singletons(QC-failed)	0	0
% Singleton	1.9300	2.6700
Diff. Chroms	606634	1200583
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	17143354	15792602
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	106283	138108
Paired Opt. Dupes	2311	676
% Dupes/100	0.0062	0.0087

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	17142713	15791243
Distinct Read Pairs	17036433	15653151
One Read Pair	16930707	15516083
Two Read Pairs	105175	136050
NRF = Distinct/Total	0.9938	0.9913
PBC1 = OnePair/Distinct	0.9938	0.9912
PBC2 = OnePair/TwoPair	160.9765	114.0469

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	34074142	31308988
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	34074142	31308988
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	34074142	31308988
Paired(QC-failed)	0	0
Read1	17037071	15654494
Read1(QC-failed)	0	0
Read2	17037071	15654494
Read2(QC-failed)	0	0
Properly Paired	34074142	31308988
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	34074142	31308988
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	138675
Np	0
N optimal	138675
N conservative	138675
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.	225
Corr. Est. Fragment Len.	0.2265
Phantom Peak	50
Corr. Phantom Peak	0.2116
Argmin. Corr.	1500
Min. Corr.	0.1947
NSC	1.1637
RSC	1.8804

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	0.3989

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	0.0934
AUC	0.4930
CHANCE divergence	0.5045
Elbow Point	0.0000
JS Distance	0.7667
Synthetic AUC	0.4999
Synthetic Elbow Point	0.2038
Synthetic JS Distance	0.4679