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Report generated at 2019-11-03 15:10:11

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	114644418	149933526
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	104610128	146624545
Mapped(QC-failed)	0	0
% Mapped	91.2500	97.7900
Paired	114644418	149933526
Paired(QC-failed)	0	0
Read1	57322209	74966763
Read1(QC-failed)	0	0
Read2	57322209	74966763
Read2(QC-failed)	0	0
Properly Paired	102855594	143525972
Properly Paired(QC-failed)	0	0
% Properly Paired	89.7200	95.7300
With itself	103871689	145761822
With itself(QC-failed)	0	0
Singletons	738439	862723
Singletons(QC-failed)	0	0
% Singleton	0.6400	0.5800
Diff. Chroms	258859	564786
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	44311750	63655918
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	905608	1138162
Paired Opt. Dupes	17832	22681
% Dupes/100	0.0204	0.0179

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	44310680	63588650
Distinct Read Pairs	43405100	62452487
One Read Pair	42514569	61334967
Two Read Pairs	875746	1100229
NRF = Distinct/Total	0.9796	0.9821
PBC1 = OnePair/Distinct	0.9795	0.9821
PBC2 = OnePair/TwoPair	48.5467	55.7475

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	86812284	125035512
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	86812284	125035512
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	86812284	125035512
Paired(QC-failed)	0	0
Read1	43406142	62517756
Read1(QC-failed)	0	0
Read2	43406142	62517756
Read2(QC-failed)	0	0
Properly Paired	86812284	125035512
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	86812284	125035512
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	157419
Np	0
N optimal	157419
N conservative	157419
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.	120
Corr. Est. Fragment Len.	0.1871
Phantom Peak	50
Corr. Phantom Peak	0.2077
Argmin. Corr.	1500
Min. Corr.	0.1784
NSC	1.0487
RSC	0.2965

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	0.2041

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	0.2692
AUC	0.4956
CHANCE divergence	0.1032
Elbow Point	0.0000
JS Distance	0.6329
Synthetic AUC	0.4994
Synthetic Elbow Point	0.1791
Synthetic JS Distance	0.2976