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Report generated at 2020-05-31 04:29:20

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	118347422	246240780
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	116663639	242844910
Mapped(QC-failed)	0	0
% Mapped	98.5800	98.6200
Paired	118347422	246240780
Paired(QC-failed)	0	0
Read1	59173711	123120390
Read1(QC-failed)	0	0
Read2	59173711	123120390
Read2(QC-failed)	0	0
Properly Paired	114152991	234365232
Properly Paired(QC-failed)	0	0
% Properly Paired	96.4600	95.1800
With itself	116140015	241490309
With itself(QC-failed)	0	0
Singletons	523624	1354601
Singletons(QC-failed)	0	0
% Singleton	0.4400	0.5500
Diff. Chroms	60252	217954
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	51950629	104467932
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	5968155	1214384
Paired Opt. Dupes	3266	3855
% Dupes/100	0.1149	0.0116

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	51941286	104430742
Distinct Read Pairs	45974223	103222930
One Read Pair	40725967	102080800
Two Read Pairs	4713021	1115539
NRF = Distinct/Total	0.8851	0.9884
PBC1 = OnePair/Distinct	0.8858	0.9889
PBC2 = OnePair/TwoPair	8.6412	91.5081

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	91964948	206507096
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	91964948	206507096
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	91964948	206507096
Paired(QC-failed)	0	0
Read1	45982474	103253548
Read1(QC-failed)	0	0
Read2	45982474	103253548
Read2(QC-failed)	0	0
Properly Paired	91964948	206507096
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	91964948	206507096
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	71269
Np	0
N optimal	71269
N conservative	71269
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.	0.2071
Phantom Peak	50
Corr. Phantom Peak	0.1758
Argmin. Corr.	1500
Min. Corr.	0.1586
NSC	1.3062
RSC	2.8181

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	0.2435

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	0.2471
AUC	0.4958
CHANCE divergence	0.1074
Elbow Point	0.0000
JS Distance	0.6723
Synthetic AUC	0.4976
Synthetic Elbow Point	0.2683
Synthetic JS Distance	0.3603