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Report generated at 2021-06-17 20:09:41

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	82191926	90394550
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	78700215	88838710
Mapped(QC-failed)	0	0
% Mapped	95.7500	98.2800
Paired	82191926	90394550
Paired(QC-failed)	0	0
Read1	41095963	45197275
Read1(QC-failed)	0	0
Read2	41095963	45197275
Read2(QC-failed)	0	0
Properly Paired	77820521	86709171
Properly Paired(QC-failed)	0	0
% Properly Paired	94.6800	95.9200
With itself	78408190	88282340
With itself(QC-failed)	0	0
Singletons	292025	556370
Singletons(QC-failed)	0	0
% Singleton	0.3600	0.6200
Diff. Chroms	37230	203772
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	35784997	37228747
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4539229	148455
Paired Opt. Dupes	40797	66499
% Dupes/100	0.1268	0.0040

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	35783910	37228110
Distinct Read Pairs	31244792	37079658
One Read Pair	27429764	36935959
Two Read Pairs	3315920	141411
NRF = Distinct/Total	0.8732	0.9960
PBC1 = OnePair/Distinct	0.8779	0.9961
PBC2 = OnePair/TwoPair	8.2721	261.1958

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	62491536	74160584
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	62491536	74160584
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	62491536	74160584
Paired(QC-failed)	0	0
Read1	31245768	37080292
Read1(QC-failed)	0	0
Read2	31245768	37080292
Read2(QC-failed)	0	0
Properly Paired	62491536	74160584
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	62491536	74160584
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	116185
Np	0
N optimal	116185
N conservative	116185
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.	145
Corr. Est. Fragment Len.	0.2758
Phantom Peak	55
Corr. Phantom Peak	0.1868
Argmin. Corr.	1500
Min. Corr.	0.1406
NSC	1.9615
RSC	2.9236

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	0.4988

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	0.1420
AUC	0.4947
CHANCE divergence	0.1670
Elbow Point	0.0000
JS Distance	0.8299
Synthetic AUC	0.4996
Synthetic Elbow Point	0.4162
Synthetic JS Distance	0.5247