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Report generated at 2020-05-10 22:02:03

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	129263032	94394890
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	123441646	90679650
Mapped(QC-failed)	0	0
% Mapped	95.5000	96.0600
Paired	129263032	94394890
Paired(QC-failed)	0	0
Read1	64631516	47197445
Read1(QC-failed)	0	0
Read2	64631516	47197445
Read2(QC-failed)	0	0
Properly Paired	119534039	85747226
Properly Paired(QC-failed)	0	0
% Properly Paired	92.4700	90.8400
With itself	121875258	88391054
With itself(QC-failed)	0	0
Singletons	1566388	2288596
Singletons(QC-failed)	0	0
% Singleton	1.2100	2.4200
Diff. Chroms	1686859	1671322
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	52625873	36214131
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1332885	344208
Paired Opt. Dupes	11148	1746
% Dupes/100	0.0253	0.0095

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	52623914	36209957
Distinct Read Pairs	51291078	35865787
One Read Pair	49986407	35524443
Two Read Pairs	1277013	338545
NRF = Distinct/Total	0.9747	0.9905
PBC1 = OnePair/Distinct	0.9746	0.9905
PBC2 = OnePair/TwoPair	39.1432	104.9327

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	102585976	71739846
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	102585976	71739846
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	102585976	71739846
Paired(QC-failed)	0	0
Read1	51292988	35869923
Read1(QC-failed)	0	0
Read2	51292988	35869923
Read2(QC-failed)	0	0
Properly Paired	102585976	71739846
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	102585976	71739846
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	45046
Np	0
N optimal	45046
N conservative	45046
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.	260
Corr. Est. Fragment Len.	0.2062
Phantom Peak	50
Corr. Phantom Peak	0.2078
Argmin. Corr.	1500
Min. Corr.	0.1802
NSC	1.1443
RSC	0.9420

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	0.2041

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	0.2119
AUC	0.4960
CHANCE divergence	0.1780
Elbow Point	0.0000
JS Distance	0.6150
Synthetic AUC	0.5055
Synthetic Elbow Point	0.1969
Synthetic JS Distance	0.3841