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Report generated at 2020-05-20 12:52:17

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	117624590	153294506
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	115978559	151246523
Mapped(QC-failed)	0	0
% Mapped	98.6000	98.6600
Paired	117624590	153294506
Paired(QC-failed)	0	0
Read1	58812295	76647253
Read1(QC-failed)	0	0
Read2	58812295	76647253
Read2(QC-failed)	0	0
Properly Paired	114658352	146129190
Properly Paired(QC-failed)	0	0
% Properly Paired	97.4800	95.3300
With itself	115582934	150686641
With itself(QC-failed)	0	0
Singletons	395625	559882
Singletons(QC-failed)	0	0
% Singleton	0.3400	0.3700
Diff. Chroms	18130	216394
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	54689635	65216723
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	10735507	700633
Paired Opt. Dupes	1383	4831
% Dupes/100	0.1963	0.0107

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	54685654	65207286
Distinct Read Pairs	43950900	64507476
One Read Pair	36650971	63842648
Two Read Pairs	5538729	647041
NRF = Distinct/Total	0.8037	0.9893
PBC1 = OnePair/Distinct	0.8339	0.9897
PBC2 = OnePair/TwoPair	6.6172	98.6686

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	87908256	129032180
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	87908256	129032180
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	87908256	129032180
Paired(QC-failed)	0	0
Read1	43954128	64516090
Read1(QC-failed)	0	0
Read2	43954128	64516090
Read2(QC-failed)	0	0
Properly Paired	87908256	129032180
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	87908256	129032180
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	169303
Np	0
N optimal	169303
N conservative	169303
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.	150
Corr. Est. Fragment Len.	0.3523
Phantom Peak	55
Corr. Phantom Peak	0.2176
Argmin. Corr.	1500
Min. Corr.	0.1599
NSC	2.2033
RSC	3.3329

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	0.7705

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	0.0531
AUC	0.4957
CHANCE divergence	0.4107
Elbow Point	0.0000
JS Distance	0.8788
Synthetic AUC	0.5011
Synthetic Elbow Point	0.5606
Synthetic JS Distance	0.6664