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Report generated at 2020-05-18 19:56:09

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	137907746	137038710
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	129908391	132965142
Mapped(QC-failed)	0	0
% Mapped	94.2000	97.0300
Paired	137907746	137038710
Paired(QC-failed)	0	0
Read1	68953873	68519355
Read1(QC-failed)	0	0
Read2	68953873	68519355
Read2(QC-failed)	0	0
Properly Paired	127889525	130403765
Properly Paired(QC-failed)	0	0
% Properly Paired	92.7400	95.1600
With itself	129073691	132147488
With itself(QC-failed)	0	0
Singletons	834700	817654
Singletons(QC-failed)	0	0
% Singleton	0.6100	0.6000
Diff. Chroms	606839	1017994
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	56008074	56489373
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	323198	246609
Paired Opt. Dupes	1351	1947
% Dupes/100	0.0058	0.0044

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	56001125	56440954
Distinct Read Pairs	55677982	56195118
One Read Pair	55356860	55950441
Two Read Pairs	319115	243541
NRF = Distinct/Total	0.9942	0.9956
PBC1 = OnePair/Distinct	0.9942	0.9956
PBC2 = OnePair/TwoPair	173.4699	229.7373

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	111369752	112485528
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	111369752	112485528
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	111369752	112485528
Paired(QC-failed)	0	0
Read1	55684876	56242764
Read1(QC-failed)	0	0
Read2	55684876	56242764
Read2(QC-failed)	0	0
Properly Paired	111369752	112485528
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	111369752	112485528
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	195378
Np	0
N optimal	195378
N conservative	195378
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.	0.1875
Phantom Peak	50
Corr. Phantom Peak	0.2060
Argmin. Corr.	1500
Min. Corr.	0.1790
NSC	1.0472
RSC	0.3140

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	0.2321

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	0.2561
AUC	0.4961
CHANCE divergence	0.0976
Elbow Point	0.0000
JS Distance	0.6685
Synthetic AUC	0.5034
Synthetic Elbow Point	0.1344
Synthetic JS Distance	0.3247