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Report generated at 2021-10-21 03:34:23

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	108051434	271900510
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	106091425	268867859
Mapped(QC-failed)	0	0
% Mapped	98.1900	98.8800
Paired	108051434	271900510
Paired(QC-failed)	0	0
Read1	54025717	135950255
Read1(QC-failed)	0	0
Read2	54025717	135950255
Read2(QC-failed)	0	0
Properly Paired	103366657	243997757
Properly Paired(QC-failed)	0	0
% Properly Paired	95.6600	89.7400
With itself	104622637	266848954
With itself(QC-failed)	0	0
Singletons	1468788	2018905
Singletons(QC-failed)	0	0
% Singleton	1.3600	0.7400
Diff. Chroms	755525	17720672
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	43967461	102422784
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4167131	6269067
Paired Opt. Dupes	7657	15041
% Dupes/100	0.0948	0.0612

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	43966555	102104617
Distinct Read Pairs	39799506	95885343
One Read Pair	35983336	90031317
Two Read Pairs	3491384	5511626
NRF = Distinct/Total	0.9052	0.9391
PBC1 = OnePair/Distinct	0.9041	0.9389
PBC2 = OnePair/TwoPair	10.3063	16.3348

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	79600660	192307434
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	79600660	192307434
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	79600660	192307434
Paired(QC-failed)	0	0
Read1	39800330	96153717
Read1(QC-failed)	0	0
Read2	39800330	96153717
Read2(QC-failed)	0	0
Properly Paired	79600660	192307434
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	79600660	192307434
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	157161
Np	0
N optimal	157161
N conservative	157161
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.	195
Corr. Est. Fragment Len.	0.2014
Phantom Peak	50
Corr. Phantom Peak	0.2010
Argmin. Corr.	1500
Min. Corr.	0.1947
NSC	1.0343
RSC	1.0476

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	0.6184

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	0.1272
AUC	0.4944
CHANCE divergence	0.1878
Elbow Point	0.0000
JS Distance	0.8072
Synthetic AUC	0.5048
Synthetic Elbow Point	0.4500
Synthetic JS Distance	0.5290