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Report generated at 2020-05-14 06:06:12

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	72016404	85104728
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	65795777	81834549
Mapped(QC-failed)	0	0
% Mapped	91.3600	96.1600
Paired	72016404	85104728
Paired(QC-failed)	0	0
Read1	36008202	42552364
Read1(QC-failed)	0	0
Read2	36008202	42552364
Read2(QC-failed)	0	0
Properly Paired	63627988	77417456
Properly Paired(QC-failed)	0	0
% Properly Paired	88.3500	90.9700
With itself	64506439	79446512
With itself(QC-failed)	0	0
Singletons	1289338	2388037
Singletons(QC-failed)	0	0
% Singleton	1.7900	2.8100
Diff. Chroms	575400	1421679
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	27512660	32647563
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	373245	620344
Paired Opt. Dupes	1576	1489
% Dupes/100	0.0136	0.0190

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	27512019	32646807
Distinct Read Pairs	27138781	32026480
One Read Pair	26769770	31415922
Two Read Pairs	364833	600925
NRF = Distinct/Total	0.9864	0.9810
PBC1 = OnePair/Distinct	0.9864	0.9809
PBC2 = OnePair/TwoPair	73.3754	52.2793

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	54278830	64054438
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	54278830	64054438
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	54278830	64054438
Paired(QC-failed)	0	0
Read1	27139415	32027219
Read1(QC-failed)	0	0
Read2	27139415	32027219
Read2(QC-failed)	0	0
Properly Paired	54278830	64054438
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	54278830	64054438
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	148819
Np	0
N optimal	148819
N conservative	148819
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.	235
Corr. Est. Fragment Len.	0.2147
Phantom Peak	50
Corr. Phantom Peak	0.2072
Argmin. Corr.	1500
Min. Corr.	0.1919
NSC	1.1186
RSC	1.4916

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	0.3373

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	0.1142
AUC	0.4944
CHANCE divergence	0.4222
Elbow Point	0.0000
JS Distance	0.7411
Synthetic AUC	0.5029
Synthetic Elbow Point	0.1681
Synthetic JS Distance	0.4586