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Report generated at 2020-05-30 19:32:35

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	100400806	180205796
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	99662023	177256106
Mapped(QC-failed)	0	0
% Mapped	99.2600	98.3600
Paired	100400806	180205796
Paired(QC-failed)	0	0
Read1	50200403	90102898
Read1(QC-failed)	0	0
Read2	50200403	90102898
Read2(QC-failed)	0	0
Properly Paired	99087248	170638535
Properly Paired(QC-failed)	0	0
% Properly Paired	98.6900	94.6900
With itself	99189520	176150889
With itself(QC-failed)	0	0
Singletons	472503	1105217
Singletons(QC-failed)	0	0
% Singleton	0.4700	0.6100
Diff. Chroms	18915	331135
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	47037943	75018495
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2196798	1307884
Paired Opt. Dupes	2667	2748
% Dupes/100	0.0467	0.0174

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	47033557	75016341
Distinct Read Pairs	44836941	73708541
One Read Pair	43079774	72495155
Two Read Pairs	1507401	1155402
NRF = Distinct/Total	0.9533	0.9826
PBC1 = OnePair/Distinct	0.9608	0.9835
PBC2 = OnePair/TwoPair	28.5788	62.7445

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	89682290	147421222
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	89682290	147421222
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	89682290	147421222
Paired(QC-failed)	0	0
Read1	44841145	73710611
Read1(QC-failed)	0	0
Read2	44841145	73710611
Read2(QC-failed)	0	0
Properly Paired	89682290	147421222
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	89682290	147421222
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	113419
Np	0
N optimal	113419
N conservative	113419
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.	160
Corr. Est. Fragment Len.	0.2921
Phantom Peak	55
Corr. Phantom Peak	0.2288
Argmin. Corr.	1500
Min. Corr.	0.1890
NSC	1.5457
RSC	2.5919

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	0.7484

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	0.0658
AUC	0.4957
CHANCE divergence	0.2707
Elbow Point	0.0000
JS Distance	0.8848
Synthetic AUC	0.4977
Synthetic Elbow Point	0.5754
Synthetic JS Distance	0.6696