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Report generated at 2021-12-04 22:04:04

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	98413794	115682520
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	88709269	110134967
Mapped(QC-failed)	0	0
% Mapped	90.1400	95.2000
Paired	98413794	115682520
Paired(QC-failed)	0	0
Read1	49206897	57841260
Read1(QC-failed)	0	0
Read2	49206897	57841260
Read2(QC-failed)	0	0
Properly Paired	79828103	104877577
Properly Paired(QC-failed)	0	0
% Properly Paired	81.1100	90.6600
With itself	80851509	106096677
With itself(QC-failed)	0	0
Singletons	7857760	4038290
Singletons(QC-failed)	0	0
% Singleton	7.9800	3.4900
Diff. Chroms	571939	752647
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	31443552	44143515
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	309836	1315729
Paired Opt. Dupes	2367	4867
% Dupes/100	0.0099	0.0298

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	31443103	44113008
Distinct Read Pairs	31133269	42798457
One Read Pair	30833265	41528318
Two Read Pairs	293265	1233455
NRF = Distinct/Total	0.9901	0.9702
PBC1 = OnePair/Distinct	0.9904	0.9703
PBC2 = OnePair/TwoPair	105.1379	33.6683

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	62267432	85655572
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	62267432	85655572
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	62267432	85655572
Paired(QC-failed)	0	0
Read1	31133716	42827786
Read1(QC-failed)	0	0
Read2	31133716	42827786
Read2(QC-failed)	0	0
Properly Paired	62267432	85655572
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	62267432	85655572
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	24737
Np	0
N optimal	24737
N conservative	24737
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.	-15
Corr. Est. Fragment Len.	0.1812
Phantom Peak	50
Corr. Phantom Peak	0.2054
Argmin. Corr.	1500
Min. Corr.	0.1762
NSC	1.0283
RSC	0.1708

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	0.0168

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	0.3056
AUC	0.4948
CHANCE divergence	0.1101
Elbow Point	0.0000
JS Distance	0.5320
Synthetic AUC	0.5090
Synthetic Elbow Point	0.0463
Synthetic JS Distance	0.2316