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Report generated at 2020-05-13 14:07:25

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	76179588	65266666
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	68676408	62068581
Mapped(QC-failed)	0	0
% Mapped	90.1500	95.1000
Paired	76179588	65266666
Paired(QC-failed)	0	0
Read1	38089794	32633333
Read1(QC-failed)	0	0
Read2	38089794	32633333
Read2(QC-failed)	0	0
Properly Paired	66914360	52881751
Properly Paired(QC-failed)	0	0
% Properly Paired	87.8400	81.0200
With itself	67792520	60433888
With itself(QC-failed)	0	0
Singletons	883888	1634693
Singletons(QC-failed)	0	0
% Singleton	1.1600	2.5000
Diff. Chroms	580607	5291648
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	29808004	20779273
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	285390	269236
Paired Opt. Dupes	3369	2954
% Dupes/100	0.0096	0.0130

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	29807467	20779235
Distinct Read Pairs	29522083	20509999
One Read Pair	29239031	20243741
Two Read Pairs	280734	263299
NRF = Distinct/Total	0.9904	0.9870
PBC1 = OnePair/Distinct	0.9904	0.9870
PBC2 = OnePair/TwoPair	104.1521	76.8850

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	59045228	41020074
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	59045228	41020074
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	59045228	41020074
Paired(QC-failed)	0	0
Read1	29522614	20510037
Read1(QC-failed)	0	0
Read2	29522614	20510037
Read2(QC-failed)	0	0
Properly Paired	59045228	41020074
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	59045228	41020074
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	172466
Np	0
N optimal	172466
N conservative	172466
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.	255
Corr. Est. Fragment Len.	0.1975
Phantom Peak	50
Corr. Phantom Peak	0.1936
Argmin. Corr.	1500
Min. Corr.	0.1809
NSC	1.0917
RSC	1.3043

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	0.1832

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	0.1377
AUC	0.4947
CHANCE divergence	0.4011
Elbow Point	0.0000
JS Distance	0.6992
Synthetic AUC	0.5038
Synthetic Elbow Point	0.0401
Synthetic JS Distance	0.4086