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Report generated at 2020-07-09 16:16:00

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	61661150	131098510
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	55150345	129303333
Mapped(QC-failed)	0	0
% Mapped	89.4400	98.6300
Paired	61661150	131098510
Paired(QC-failed)	0	0
Read1	30830575	65549255
Read1(QC-failed)	0	0
Read2	30830575	65549255
Read2(QC-failed)	0	0
Properly Paired	54762733	124505591
Properly Paired(QC-failed)	0	0
% Properly Paired	88.8100	94.9700
With itself	54922123	128591289
With itself(QC-failed)	0	0
Singletons	228222	712044
Singletons(QC-failed)	0	0
% Singleton	0.3700	0.5400
Diff. Chroms	22179	201152
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	25440994	54582151
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2954354	411333
Paired Opt. Dupes	1300	2925
% Dupes/100	0.1161	0.0075

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	25434099	54552078
Distinct Read Pairs	22480665	54144593
One Read Pair	19905985	53754757
Two Read Pairs	2289622	382787
NRF = Distinct/Total	0.8839	0.9925
PBC1 = OnePair/Distinct	0.8855	0.9928
PBC2 = OnePair/TwoPair	8.6940	140.4299

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	44973280	108341636
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	44973280	108341636
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	44973280	108341636
Paired(QC-failed)	0	0
Read1	22486640	54170818
Read1(QC-failed)	0	0
Read2	22486640	54170818
Read2(QC-failed)	0	0
Properly Paired	44973280	108341636
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	44973280	108341636
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	115539
Np	0
N optimal	115539
N conservative	115539
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.	0.2407
Phantom Peak	55
Corr. Phantom Peak	0.1861
Argmin. Corr.	1500
Min. Corr.	0.1524
NSC	1.5789
RSC	2.6213

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	0.4993

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	0.1396
AUC	0.4939
CHANCE divergence	0.2030
Elbow Point	0.0000
JS Distance	0.8151
Synthetic AUC	0.4981
Synthetic Elbow Point	0.4171
Synthetic JS Distance	0.5095