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Report generated at 2019-11-01 21:46:37

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	277368334	345403306
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	273211054	341696882
Mapped(QC-failed)	0	0
% Mapped	98.5000	98.9300
Paired	277368334	345403306
Paired(QC-failed)	0	0
Read1	138684167	172701653
Read1(QC-failed)	0	0
Read2	138684167	172701653
Read2(QC-failed)	0	0
Properly Paired	267245645	332198812
Properly Paired(QC-failed)	0	0
% Properly Paired	96.3500	96.1800
With itself	271139287	339827021
With itself(QC-failed)	0	0
Singletons	2071767	1869861
Singletons(QC-failed)	0	0
% Singleton	0.7500	0.5400
Diff. Chroms	2481092	4989385
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	110284059	139165923
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	13214164	13769945
Paired Opt. Dupes	30842	20499
% Dupes/100	0.1198	0.0989

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	110281253	139068773
Distinct Read Pairs	97067408	125309978
One Read Pair	85201285	112707049
Two Read Pairs	10641704	11538367
NRF = Distinct/Total	0.8802	0.9011
PBC1 = OnePair/Distinct	0.8778	0.8994
PBC2 = OnePair/TwoPair	8.0064	9.7680

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	194139790	250791956
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	194139790	250791956
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	194139790	250791956
Paired(QC-failed)	0	0
Read1	97069895	125395978
Read1(QC-failed)	0	0
Read2	97069895	125395978
Read2(QC-failed)	0	0
Properly Paired	194139790	250791956
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	194139790	250791956
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	205268
Np	0
N optimal	205268
N conservative	205268
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.	140
Corr. Est. Fragment Len.	0.1746
Phantom Peak	50
Corr. Phantom Peak	0.1786
Argmin. Corr.	1500
Min. Corr.	0.1725
NSC	1.0117
RSC	0.3336

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	0.1443

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	0.2646
AUC	0.4964
CHANCE divergence	0.1033
Elbow Point	0.0000
JS Distance	0.5621
Synthetic AUC	0.4977
Synthetic Elbow Point	0.1958
Synthetic JS Distance	0.3138