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Report generated at 2019-11-01 01:57:32

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	106128300	345403306
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	103494153	341696882
Mapped(QC-failed)	0	0
% Mapped	97.5200	98.9300
Paired	106128300	345403306
Paired(QC-failed)	0	0
Read1	53064150	172701653
Read1(QC-failed)	0	0
Read2	53064150	172701653
Read2(QC-failed)	0	0
Properly Paired	102212492	332198812
Properly Paired(QC-failed)	0	0
% Properly Paired	96.3100	96.1800
With itself	102890087	339827021
With itself(QC-failed)	0	0
Singletons	604066	1869861
Singletons(QC-failed)	0	0
% Singleton	0.5700	0.5400
Diff. Chroms	359361	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	44748050	139165923
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	8104422	13769945
Paired Opt. Dupes	8880	20499
% Dupes/100	0.1811	0.0989

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	44744003	139068773
Distinct Read Pairs	36640275	125309978
One Read Pair	29759568	112707049
Two Read Pairs	5818155	11538367
NRF = Distinct/Total	0.8189	0.9011
PBC1 = OnePair/Distinct	0.8122	0.8994
PBC2 = OnePair/TwoPair	5.1149	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	73287256	250791956
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	73287256	250791956
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	73287256	250791956
Paired(QC-failed)	0	0
Read1	36643628	125395978
Read1(QC-failed)	0	0
Read2	36643628	125395978
Read2(QC-failed)	0	0
Properly Paired	73287256	250791956
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	73287256	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	104009
Np	0
N optimal	104009
N conservative	104009
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.	195
Corr. Est. Fragment Len.	0.2127
Phantom Peak	55
Corr. Phantom Peak	0.2070
Argmin. Corr.	1500
Min. Corr.	0.1744
NSC	1.2198
RSC	1.1772

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	0.3806

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	0.1939
AUC	0.4942
CHANCE divergence	0.1244
Elbow Point	0.0000
JS Distance	0.7699
Synthetic AUC	0.4960
Synthetic Elbow Point	0.3579
Synthetic JS Distance	0.4327