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Report generated at 2019-10-13 04:57:04

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	91725664	112182380
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	88985699	109790255
Mapped(QC-failed)	0	0
% Mapped	97.0100	97.8700
Paired	91725664	112182380
Paired(QC-failed)	0	0
Read1	45862832	56091190
Read1(QC-failed)	0	0
Read2	45862832	56091190
Read2(QC-failed)	0	0
Properly Paired	88215827	108525037
Properly Paired(QC-failed)	0	0
% Properly Paired	96.1700	96.7400
With itself	88547133	109236441
With itself(QC-failed)	0	0
Singletons	438566	553814
Singletons(QC-failed)	0	0
% Singleton	0.4800	0.4900
Diff. Chroms	114576	375641
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	39289568	47985507
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	21604644	3406633
Paired Opt. Dupes	7695	6387
% Dupes/100	0.5499	0.0710

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	39288749	47950820
Distinct Read Pairs	17684530	44546891
One Read Pair	8317144	41387028
Two Read Pairs	4205230	2937039
NRF = Distinct/Total	0.4501	0.9290
PBC1 = OnePair/Distinct	0.4703	0.9291
PBC2 = OnePair/TwoPair	1.9778	14.0914

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	35369848	89157748
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	35369848	89157748
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	35369848	89157748
Paired(QC-failed)	0	0
Read1	17684924	44578874
Read1(QC-failed)	0	0
Read2	17684924	44578874
Read2(QC-failed)	0	0
Properly Paired	35369848	89157748
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	35369848	89157748
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	65813
Np	0
N optimal	65813
N conservative	65813
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.	0.1196
Phantom Peak	50
Corr. Phantom Peak	0.1214
Argmin. Corr.	1500
Min. Corr.	0.1145
NSC	1.0441
RSC	0.7321

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	0.0554

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	0.2565
AUC	0.4931
CHANCE divergence	0.1653
Elbow Point	0.0000
JS Distance	0.5776
Synthetic AUC	0.5015
Synthetic Elbow Point	0.1023
Synthetic JS Distance	0.2795