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Report generated at 2021-02-02 20:51:51

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	124697314	98018842
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	123222621	96270768
Mapped(QC-failed)	0	0
% Mapped	98.8200	98.2200
Paired	124697314	98018842
Paired(QC-failed)	0	0
Read1	62348657	49009421
Read1(QC-failed)	0	0
Read2	62348657	49009421
Read2(QC-failed)	0	0
Properly Paired	121054050	94403324
Properly Paired(QC-failed)	0	0
% Properly Paired	97.0800	96.3100
With itself	122438014	95481141
With itself(QC-failed)	0	0
Singletons	784607	789627
Singletons(QC-failed)	0	0
% Singleton	0.6300	0.8100
Diff. Chroms	101506	119737
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	52655922	40573634
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	752261	190324
Paired Opt. Dupes	1013	892
% Dupes/100	0.0143	0.0047

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	52627090	40559437
Distinct Read Pairs	51876885	40369743
One Read Pair	51140267	40192163
Two Read Pairs	724804	172878
NRF = Distinct/Total	0.9857	0.9953
PBC1 = OnePair/Distinct	0.9858	0.9956
PBC2 = OnePair/TwoPair	70.5574	232.4886

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	103807322	80766620
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	103807322	80766620
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	103807322	80766620
Paired(QC-failed)	0	0
Read1	51903661	40383310
Read1(QC-failed)	0	0
Read2	51903661	40383310
Read2(QC-failed)	0	0
Properly Paired	103807322	80766620
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	103807322	80766620
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	168091
Np	0
N optimal	168091
N conservative	168091
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.	125
Corr. Est. Fragment Len.	0.1750
Phantom Peak	50
Corr. Phantom Peak	0.1759
Argmin. Corr.	1500
Min. Corr.	0.1682
NSC	1.0406
RSC	0.8840

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	0.1129

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	0.2822
AUC	0.4959
CHANCE divergence	0.1015
Elbow Point	0.0000
JS Distance	0.6042
Synthetic AUC	0.5017
Synthetic Elbow Point	0.0634
Synthetic JS Distance	0.2750