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Report generated at 2020-07-10 03:09:35

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	134245220	136244046
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	132466836	134324819
Mapped(QC-failed)	0	0
% Mapped	98.6800	98.5900
Paired	134245220	136244046
Paired(QC-failed)	0	0
Read1	67122610	68122023
Read1(QC-failed)	0	0
Read2	67122610	68122023
Read2(QC-failed)	0	0
Properly Paired	130872467	131038518
Properly Paired(QC-failed)	0	0
% Properly Paired	97.4900	96.1800
With itself	131824402	133591989
With itself(QC-failed)	0	0
Singletons	642434	732830
Singletons(QC-failed)	0	0
% Singleton	0.4800	0.5400
Diff. Chroms	83775	172253
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	57130210	57476635
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	812221	368798
Paired Opt. Dupes	2635	2996
% Dupes/100	0.0142	0.0064

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	57094487	57449552
Distinct Read Pairs	56285124	57083273
One Read Pair	55492766	56730634
Two Read Pairs	779379	346986
NRF = Distinct/Total	0.9858	0.9936
PBC1 = OnePair/Distinct	0.9859	0.9938
PBC2 = OnePair/TwoPair	71.2013	163.4955

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	112635978	114215674
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	112635978	114215674
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	112635978	114215674
Paired(QC-failed)	0	0
Read1	56317989	57107837
Read1(QC-failed)	0	0
Read2	56317989	57107837
Read2(QC-failed)	0	0
Properly Paired	112635978	114215674
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	112635978	114215674
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	104499
Np	0
N optimal	104499
N conservative	104499
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.	145
Corr. Est. Fragment Len.	0.1773
Phantom Peak	50
Corr. Phantom Peak	0.1829
Argmin. Corr.	1500
Min. Corr.	0.1727
NSC	1.0266
RSC	0.4511

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	0.0581

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	0.3007
AUC	0.4962
CHANCE divergence	0.0983
Elbow Point	0.0000
JS Distance	0.5669
Synthetic AUC	0.4986
Synthetic Elbow Point	0.0965
Synthetic JS Distance	0.2462