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Report generated at 2019-10-30 14:31:14

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	85658256	140993220
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	81727197	139041098
Mapped(QC-failed)	0	0
% Mapped	95.4100	98.6200
Paired	85658256	140993220
Paired(QC-failed)	0	0
Read1	42829128	70496610
Read1(QC-failed)	0	0
Read2	42829128	70496610
Read2(QC-failed)	0	0
Properly Paired	80084767	134740908
Properly Paired(QC-failed)	0	0
% Properly Paired	93.4900	95.5700
With itself	81154113	138315977
With itself(QC-failed)	0	0
Singletons	573084	725121
Singletons(QC-failed)	0	0
% Singleton	0.6700	0.5100
Diff. Chroms	647135	2179951
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	34762944	56499814
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1199391	1540164
Paired Opt. Dupes	13685	14091
% Dupes/100	0.0345	0.0273

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	34762701	56486240
Distinct Read Pairs	33563323	54946507
One Read Pair	32398885	53441534
Two Read Pairs	1130427	1471338
NRF = Distinct/Total	0.9655	0.9727
PBC1 = OnePair/Distinct	0.9653	0.9726
PBC2 = OnePair/TwoPair	28.6607	36.3217

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	67127106	109919300
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	67127106	109919300
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	67127106	109919300
Paired(QC-failed)	0	0
Read1	33563553	54959650
Read1(QC-failed)	0	0
Read2	33563553	54959650
Read2(QC-failed)	0	0
Properly Paired	67127106	109919300
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	67127106	109919300
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	139444
Np	0
N optimal	139444
N conservative	139444
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.	145
Corr. Est. Fragment Len.	0.2205
Phantom Peak	50
Corr. Phantom Peak	0.2210
Argmin. Corr.	1500
Min. Corr.	0.2120
NSC	1.0402
RSC	0.9422

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	0.7234

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	0.0795
AUC	0.4941
CHANCE divergence	0.3626
Elbow Point	0.0000
JS Distance	0.8385
Synthetic AUC	0.5101
Synthetic Elbow Point	0.4905
Synthetic JS Distance	0.5928