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Report generated at 2020-05-17 21:06:10

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	72168398	91058302
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	67601399	88858777
Mapped(QC-failed)	0	0
% Mapped	93.6700	97.5800
Paired	72168398	91058302
Paired(QC-failed)	0	0
Read1	36084199	45529151
Read1(QC-failed)	0	0
Read2	36084199	45529151
Read2(QC-failed)	0	0
Properly Paired	66847677	87463672
Properly Paired(QC-failed)	0	0
% Properly Paired	92.6300	96.0500
With itself	67244224	88414762
With itself(QC-failed)	0	0
Singletons	357175	444015
Singletons(QC-failed)	0	0
% Singleton	0.4900	0.4900
Diff. Chroms	230614	473257
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	30203286	38226012
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	735243	140477
Paired Opt. Dupes	1098	1407
% Dupes/100	0.0243	0.0037

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	30179522	38152882
Distinct Read Pairs	29444937	38013834
One Read Pair	28726215	37875216
Two Read Pairs	703176	138191
NRF = Distinct/Total	0.9757	0.9964
PBC1 = OnePair/Distinct	0.9756	0.9964
PBC2 = OnePair/TwoPair	40.8521	274.0787

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	58936086	76171070
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	58936086	76171070
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	58936086	76171070
Paired(QC-failed)	0	0
Read1	29468043	38085535
Read1(QC-failed)	0	0
Read2	29468043	38085535
Read2(QC-failed)	0	0
Properly Paired	58936086	76171070
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	58936086	76171070
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	26733
Np	0
N optimal	26733
N conservative	26733
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.	220
Corr. Est. Fragment Len.	0.3369
Phantom Peak	50
Corr. Phantom Peak	0.3095
Argmin. Corr.	1500
Min. Corr.	0.1769
NSC	1.9040
RSC	1.2062

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	0.4299

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	0.1631
AUC	0.4947
CHANCE divergence	0.1449
Elbow Point	0.0000
JS Distance	0.8141
Synthetic AUC	0.5004
Synthetic Elbow Point	0.4064
Synthetic JS Distance	0.5139