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Report generated at 2020-07-14 15:08:47

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	76606808	61218190
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	71980853	56551430
Mapped(QC-failed)	0	0
% Mapped	93.9600	92.3800
Paired	76606808	61218190
Paired(QC-failed)	0	0
Read1	38303404	30609095
Read1(QC-failed)	0	0
Read2	38303404	30609095
Read2(QC-failed)	0	0
Properly Paired	68595606	43003222
Properly Paired(QC-failed)	0	0
% Properly Paired	89.5400	70.2500
With itself	70787115	54252500
With itself(QC-failed)	0	0
Singletons	1193738	2298930
Singletons(QC-failed)	0	0
% Singleton	1.5600	3.7600
Diff. Chroms	1692705	7885178
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	30485271	16203032
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	288199	229718
Paired Opt. Dupes	4535	1893
% Dupes/100	0.0095	0.0142

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	30454549	16200015
Distinct Read Pairs	30166847	15970340
One Read Pair	29881367	15743449
Two Read Pairs	283273	224151
NRF = Distinct/Total	0.9906	0.9858
PBC1 = OnePair/Distinct	0.9905	0.9858
PBC2 = OnePair/TwoPair	105.4861	70.2359

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	60394144	31946628
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	60394144	31946628
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	60394144	31946628
Paired(QC-failed)	0	0
Read1	30197072	15973314
Read1(QC-failed)	0	0
Read2	30197072	15973314
Read2(QC-failed)	0	0
Properly Paired	60394144	31946628
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	60394144	31946628
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	119149
Np	0
N optimal	119149
N conservative	119149
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.	0.1878
Phantom Peak	50
Corr. Phantom Peak	0.1928
Argmin. Corr.	1500
Min. Corr.	0.1813
NSC	1.0360
RSC	0.5681

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	0.1890

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	0.1998
AUC	0.4947
CHANCE divergence	0.1555
Elbow Point	0.0000
JS Distance	0.7010
Synthetic AUC	0.5053
Synthetic Elbow Point	0.1279
Synthetic JS Distance	0.3944