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Report generated at 2019-11-03 18:30:35

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	153503376	144885712
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	151984938	141771472
Mapped(QC-failed)	0	0
% Mapped	99.0100	97.8500
Paired	153503376	144885712
Paired(QC-failed)	0	0
Read1	76751688	72442856
Read1(QC-failed)	0	0
Read2	76751688	72442856
Read2(QC-failed)	0	0
Properly Paired	150192126	139161591
Properly Paired(QC-failed)	0	0
% Properly Paired	97.8400	96.0500
With itself	151315325	140839614
With itself(QC-failed)	0	0
Singletons	669613	931858
Singletons(QC-failed)	0	0
% Singleton	0.4400	0.6400
Diff. Chroms	482086	862243
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	68769187	61727393
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1748926	1553623
Paired Opt. Dupes	16155	14884
% Dupes/100	0.0254	0.0252

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	68766928	61648150
Distinct Read Pairs	67018059	60097677
One Read Pair	65296619	58572284
Two Read Pairs	1694524	1501098
NRF = Distinct/Total	0.9746	0.9748
PBC1 = OnePair/Distinct	0.9743	0.9746
PBC2 = OnePair/TwoPair	38.5339	39.0196

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	134040522	120347540
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	134040522	120347540
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	134040522	120347540
Paired(QC-failed)	0	0
Read1	67020261	60173770
Read1(QC-failed)	0	0
Read2	67020261	60173770
Read2(QC-failed)	0	0
Properly Paired	134040522	120347540
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	134040522	120347540
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	201812
Np	0
N optimal	201812
N conservative	201812
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.	190
Corr. Est. Fragment Len.	0.1776
Phantom Peak	50
Corr. Phantom Peak	0.1805
Argmin. Corr.	1500
Min. Corr.	0.1762
NSC	1.0079
RSC	0.3224

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	0.3989

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	0.2239
AUC	0.4965
CHANCE divergence	0.1001
Elbow Point	0.0000
JS Distance	0.7000
Synthetic AUC	0.5032
Synthetic Elbow Point	0.2509
Synthetic JS Distance	0.3747