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Report generated at 2020-07-15 14:52:57

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	185929114	103857894
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	176334374	102353291
Mapped(QC-failed)	0	0
% Mapped	94.8400	98.5500
Paired	185929114	103857894
Paired(QC-failed)	0	0
Read1	92964557	51928947
Read1(QC-failed)	0	0
Read2	92964557	51928947
Read2(QC-failed)	0	0
Properly Paired	165566791	100340149
Properly Paired(QC-failed)	0	0
% Properly Paired	89.0500	96.6100
With itself	173886802	101801899
With itself(QC-failed)	0	0
Singletons	2447572	551392
Singletons(QC-failed)	0	0
% Singleton	1.3200	0.5300
Diff. Chroms	477721	131984
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	61790457	44269160
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3438550	406091
Paired Opt. Dupes	1408	1054
% Dupes/100	0.0556	0.0092

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	61788652	44267990
Distinct Read Pairs	58350194	43861911
One Read Pair	55247163	43470849
Two Read Pairs	2906290	382881
NRF = Distinct/Total	0.9444	0.9908
PBC1 = OnePair/Distinct	0.9468	0.9911
PBC2 = OnePair/TwoPair	19.0095	113.5362

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	116703814	87726138
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	116703814	87726138
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	116703814	87726138
Paired(QC-failed)	0	0
Read1	58351907	43863069
Read1(QC-failed)	0	0
Read2	58351907	43863069
Read2(QC-failed)	0	0
Properly Paired	116703814	87726138
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	116703814	87726138
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	252621
Np	0
N optimal	252621
N conservative	252621
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.	125
Corr. Est. Fragment Len.	0.2092
Phantom Peak	50
Corr. Phantom Peak	0.2323
Argmin. Corr.	1500
Min. Corr.	0.1921
NSC	1.0889
RSC	0.4259

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	0.3465

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	0.1737
AUC	0.4962
CHANCE divergence	0.1382
Elbow Point	0.0000
JS Distance	0.7040
Synthetic AUC	0.5048
Synthetic Elbow Point	0.2912
Synthetic JS Distance	0.4572