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Report generated at 2020-05-20 13:37:21

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	97653020	153294506
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	96897594	151246523
Mapped(QC-failed)	0	0
% Mapped	99.2300	98.6600
Paired	97653020	153294506
Paired(QC-failed)	0	0
Read1	48826510	76647253
Read1(QC-failed)	0	0
Read2	48826510	76647253
Read2(QC-failed)	0	0
Properly Paired	96359296	146129190
Properly Paired(QC-failed)	0	0
% Properly Paired	98.6800	95.3300
With itself	96605500	150686641
With itself(QC-failed)	0	0
Singletons	292094	559882
Singletons(QC-failed)	0	0
% Singleton	0.3000	0.3700
Diff. Chroms	40193	216394
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	42565669	65216723
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	653632	700633
Paired Opt. Dupes	3392	4831
% Dupes/100	0.0154	0.0107

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	42555889	65207286
Distinct Read Pairs	41902684	64507476
One Read Pair	41263302	63842648
Two Read Pairs	627710	647041
NRF = Distinct/Total	0.9847	0.9893
PBC1 = OnePair/Distinct	0.9847	0.9897
PBC2 = OnePair/TwoPair	65.7363	98.6686

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	83824074	129032180
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	83824074	129032180
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	83824074	129032180
Paired(QC-failed)	0	0
Read1	41912037	64516090
Read1(QC-failed)	0	0
Read2	41912037	64516090
Read2(QC-failed)	0	0
Properly Paired	83824074	129032180
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	83824074	129032180
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	201256
Np	0
N optimal	201256
N conservative	201256
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.	150
Corr. Est. Fragment Len.	0.1814
Phantom Peak	50
Corr. Phantom Peak	0.1809
Argmin. Corr.	1500
Min. Corr.	0.1748
NSC	1.0379
RSC	1.0712

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	0.1649

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	0.2286
AUC	0.4956
CHANCE divergence	0.1602
Elbow Point	0.0000
JS Distance	0.5980
Synthetic AUC	0.4982
Synthetic Elbow Point	0.1650
Synthetic JS Distance	0.3478