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Report generated at 2019-10-13 02:18:12

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	108582818	103045968
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	103595950	98644909
Mapped(QC-failed)	0	0
% Mapped	95.4100	95.7300
Paired	108582818	103045968
Paired(QC-failed)	0	0
Read1	54291409	51522984
Read1(QC-failed)	0	0
Read2	54291409	51522984
Read2(QC-failed)	0	0
Properly Paired	99148504	94442742
Properly Paired(QC-failed)	0	0
% Properly Paired	91.3100	91.6500
With itself	99823891	95330195
With itself(QC-failed)	0	0
Singletons	3772059	3314714
Singletons(QC-failed)	0	0
% Singleton	3.4700	3.2200
Diff. Chroms	359777	525356
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	41932821	40142171
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2919483	1418352
Paired Opt. Dupes	4534	4354
% Dupes/100	0.0696	0.0353

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	41931301	40110587
Distinct Read Pairs	39011924	38693616
One Read Pair	36270672	37331634
Two Read Pairs	2573248	1311985
NRF = Distinct/Total	0.9304	0.9647
PBC1 = OnePair/Distinct	0.9297	0.9648
PBC2 = OnePair/TwoPair	14.0953	28.4543

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	78026676	77447638
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	78026676	77447638
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	78026676	77447638
Paired(QC-failed)	0	0
Read1	39013338	38723819
Read1(QC-failed)	0	0
Read2	39013338	38723819
Read2(QC-failed)	0	0
Properly Paired	78026676	77447638
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	78026676	77447638
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	54898
Np	0
N optimal	54898
N conservative	54898
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.	0.1892
Phantom Peak	50
Corr. Phantom Peak	0.1960
Argmin. Corr.	1500
Min. Corr.	0.1712
NSC	1.1050
RSC	0.7258

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	0.1640

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	0.2810
AUC	0.4954
CHANCE divergence	0.1044
Elbow Point	0.0000
JS Distance	0.6235
Synthetic AUC	0.5042
Synthetic Elbow Point	0.1816
Synthetic JS Distance	0.2993