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Report generated at 2020-06-25 02:12:14

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	305423110	151544194
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	283529966	148910512
Mapped(QC-failed)	0	0
% Mapped	92.8300	98.2600
Paired	305423110	151544194
Paired(QC-failed)	0	0
Read1	152711555	75772097
Read1(QC-failed)	0	0
Read2	152711555	75772097
Read2(QC-failed)	0	0
Properly Paired	278750991	146074541
Properly Paired(QC-failed)	0	0
% Properly Paired	91.2700	96.3900
With itself	280862155	147974444
With itself(QC-failed)	0	0
Singletons	2667811	936068
Singletons(QC-failed)	0	0
% Singleton	0.8700	0.6200
Diff. Chroms	437395	884346
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	124949813	64801692
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	6163742	1185579
Paired Opt. Dupes	15534	14661
% Dupes/100	0.0493	0.0183

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	124946771	64733526
Distinct Read Pairs	118783226	63550092
One Read Pair	112934560	62385083
Two Read Pairs	5550339	1147263
NRF = Distinct/Total	0.9507	0.9817
PBC1 = OnePair/Distinct	0.9508	0.9817
PBC2 = OnePair/TwoPair	20.3473	54.3773

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	237572142	127232226
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	237572142	127232226
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	237572142	127232226
Paired(QC-failed)	0	0
Read1	118786071	63616113
Read1(QC-failed)	0	0
Read2	118786071	63616113
Read2(QC-failed)	0	0
Properly Paired	237572142	127232226
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	237572142	127232226
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	184536
Np	0
N optimal	184536
N conservative	184536
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.	215
Corr. Est. Fragment Len.	0.1868
Phantom Peak	50
Corr. Phantom Peak	0.1959
Argmin. Corr.	1500
Min. Corr.	0.1778
NSC	1.0505
RSC	0.4976

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	0.4195

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	0.2279
AUC	0.4974
CHANCE divergence	0.0934
Elbow Point	0.0000
JS Distance	0.7495
Synthetic AUC	0.5012
Synthetic Elbow Point	0.2737
Synthetic JS Distance	0.3810