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Report generated at 2020-12-04 00:44:27

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	64553286	193594802
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	63298703	187969057
Mapped(QC-failed)	0	0
% Mapped	98.0600	97.0900
Paired	64553286	193594802
Paired(QC-failed)	0	0
Read1	32276643	96797401
Read1(QC-failed)	0	0
Read2	32276643	96797401
Read2(QC-failed)	0	0
Properly Paired	62839111	184287983
Properly Paired(QC-failed)	0	0
% Properly Paired	97.3400	95.1900
With itself	63101057	185784698
With itself(QC-failed)	0	0
Singletons	197646	2184359
Singletons(QC-failed)	0	0
% Singleton	0.3100	1.1300
Diff. Chroms	117589	610670
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	28778550	78211821
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	390067	539110
Paired Opt. Dupes	24883	19807
% Dupes/100	0.0136	0.0069

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	28738060	77646644
Distinct Read Pairs	28348924	77172156
One Read Pair	27964871	76701136
Two Read Pairs	379036	467668
NRF = Distinct/Total	0.9865	0.9939
PBC1 = OnePair/Distinct	0.9865	0.9939
PBC2 = OnePair/TwoPair	73.7789	164.0077

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	56776966	155345422
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	56776966	155345422
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	56776966	155345422
Paired(QC-failed)	0	0
Read1	28388483	77672711
Read1(QC-failed)	0	0
Read2	28388483	77672711
Read2(QC-failed)	0	0
Properly Paired	56776966	155345422
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	56776966	155345422
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	107410
Np	0
N optimal	107410
N conservative	107410
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.	160
Corr. Est. Fragment Len.	0.2229
Phantom Peak	50
Corr. Phantom Peak	0.2160
Argmin. Corr.	1500
Min. Corr.	0.1894
NSC	1.1768
RSC	1.2570

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	0.3707

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	0.1862
AUC	0.4946
CHANCE divergence	0.1394
Elbow Point	0.0000
JS Distance	0.7541
Synthetic AUC	0.5090
Synthetic Elbow Point	0.3463
Synthetic JS Distance	0.4407