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Report generated at 2020-05-20 15:48:27

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	91156212	112353936
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	90280201	110770243
Mapped(QC-failed)	0	0
% Mapped	99.0400	98.5900
Paired	91156212	112353936
Paired(QC-failed)	0	0
Read1	45578106	56176968
Read1(QC-failed)	0	0
Read2	45578106	56176968
Read2(QC-failed)	0	0
Properly Paired	87053170	108511153
Properly Paired(QC-failed)	0	0
% Properly Paired	95.5000	96.5800
With itself	90004351	110354562
With itself(QC-failed)	0	0
Singletons	275850	415681
Singletons(QC-failed)	0	0
% Singleton	0.3000	0.3700
Diff. Chroms	74173	150895
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	38831592	48323075
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	773953	444698
Paired Opt. Dupes	2223	3241
% Dupes/100	0.0199	0.0092

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	38824182	48311362
Distinct Read Pairs	38050612	47868098
One Read Pair	37296852	47445446
Two Read Pairs	736486	412601
NRF = Distinct/Total	0.9801	0.9908
PBC1 = OnePair/Distinct	0.9802	0.9912
PBC2 = OnePair/TwoPair	50.6416	114.9911

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	76115278	95756754
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	76115278	95756754
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	76115278	95756754
Paired(QC-failed)	0	0
Read1	38057639	47878377
Read1(QC-failed)	0	0
Read2	38057639	47878377
Read2(QC-failed)	0	0
Properly Paired	76115278	95756754
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	76115278	95756754
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	150883
Np	0
N optimal	150883
N conservative	150883
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.	150
Corr. Est. Fragment Len.	0.1826
Phantom Peak	50
Corr. Phantom Peak	0.1822
Argmin. Corr.	1500
Min. Corr.	0.1727
NSC	1.0573
RSC	1.0412

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	0.1175

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	0.2479
AUC	0.4953
CHANCE divergence	0.1372
Elbow Point	0.0000
JS Distance	0.5971
Synthetic AUC	0.5061
Synthetic Elbow Point	0.1232
Synthetic JS Distance	0.3181