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Report generated at 2020-05-20 17:07:02

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	65337120	153294506
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	65096176	151246523
Mapped(QC-failed)	0	0
% Mapped	99.6300	98.6600
Paired	65337120	153294506
Paired(QC-failed)	0	0
Read1	32668560	76647253
Read1(QC-failed)	0	0
Read2	32668560	76647253
Read2(QC-failed)	0	0
Properly Paired	64931482	146129190
Properly Paired(QC-failed)	0	0
% Properly Paired	99.3800	95.3300
With itself	64975163	150686641
With itself(QC-failed)	0	0
Singletons	121013	559882
Singletons(QC-failed)	0	0
% Singleton	0.1900	0.3700
Diff. Chroms	14354	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	30557776	65216723
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1955540	700633
Paired Opt. Dupes	2593	4831
% Dupes/100	0.0640	0.0107

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	30553302	65207286
Distinct Read Pairs	28597849	64507476
One Read Pair	27198233	63842648
Two Read Pairs	1098219	647041
NRF = Distinct/Total	0.9360	0.9893
PBC1 = OnePair/Distinct	0.9511	0.9897
PBC2 = OnePair/TwoPair	24.7658	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	57204472	129032180
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	57204472	129032180
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	57204472	129032180
Paired(QC-failed)	0	0
Read1	28602236	64516090
Read1(QC-failed)	0	0
Read2	28602236	64516090
Read2(QC-failed)	0	0
Properly Paired	57204472	129032180
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	57204472	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	90000
Np	0
N optimal	90000
N conservative	90000
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.	170
Corr. Est. Fragment Len.	0.3297
Phantom Peak	40
Corr. Phantom Peak	0.2106
Argmin. Corr.	1500
Min. Corr.	0.1474
NSC	2.2377
RSC	2.8852

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	0.7782

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	0.0451
AUC	0.4946
CHANCE divergence	0.4167
Elbow Point	0.0000
JS Distance	0.9112
Synthetic AUC	0.5044
Synthetic Elbow Point	0.6197
Synthetic JS Distance	0.7027