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Report generated at 2019-10-13 06:58:00

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	112065770	125060354
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	101751794	115723438
Mapped(QC-failed)	0	0
% Mapped	90.8000	92.5300
Paired	112065770	125060354
Paired(QC-failed)	0	0
Read1	56032885	62530177
Read1(QC-failed)	0	0
Read2	56032885	62530177
Read2(QC-failed)	0	0
Properly Paired	94524929	106456049
Properly Paired(QC-failed)	0	0
% Properly Paired	84.3500	85.1200
With itself	95308545	108232132
With itself(QC-failed)	0	0
Singletons	6443249	7491306
Singletons(QC-failed)	0	0
% Singleton	5.7500	5.9900
Diff. Chroms	451380	1197727
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	37553507	42322290
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	9704521	491333
Paired Opt. Dupes	3212	3358
% Dupes/100	0.2584	0.0116

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	37552831	42292215
Distinct Read Pairs	27848486	41801473
One Read Pair	20655674	41322617
Two Read Pairs	5320549	470011
NRF = Distinct/Total	0.7416	0.9884
PBC1 = OnePair/Distinct	0.7417	0.9885
PBC2 = OnePair/TwoPair	3.8822	87.9184

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	55697972	83661914
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	55697972	83661914
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	55697972	83661914
Paired(QC-failed)	0	0
Read1	27848986	41830957
Read1(QC-failed)	0	0
Read2	27848986	41830957
Read2(QC-failed)	0	0
Properly Paired	55697972	83661914
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	55697972	83661914
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	47345
Np	0
N optimal	47345
N conservative	47345
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.	130
Corr. Est. Fragment Len.	0.1567
Phantom Peak	50
Corr. Phantom Peak	0.1662
Argmin. Corr.	1500
Min. Corr.	0.1515
NSC	1.0343
RSC	0.3528

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	0.0379

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	0.3032
AUC	0.4945
CHANCE divergence	0.1127
Elbow Point	0.0000
JS Distance	0.5399
Synthetic AUC	0.4967
Synthetic Elbow Point	0.0675
Synthetic JS Distance	0.2328