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Report generated at 2020-05-02 13:04:51

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	61583178	52392786
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	52850170	49028461
Mapped(QC-failed)	0	0
% Mapped	85.8200	93.5800
Paired	61583178	52392786
Paired(QC-failed)	0	0
Read1	30791589	26196393
Read1(QC-failed)	0	0
Read2	30791589	26196393
Read2(QC-failed)	0	0
Properly Paired	50380534	42386284
Properly Paired(QC-failed)	0	0
% Properly Paired	81.8100	80.9000
With itself	51522081	47560814
With itself(QC-failed)	0	0
Singletons	1328089	1467647
Singletons(QC-failed)	0	0
% Singleton	2.1600	2.8000
Diff. Chroms	737692	3739781
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	22035255	17509183
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	210732	332500
Paired Opt. Dupes	1987	1946
% Dupes/100	0.0096	0.0190

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	22035021	17509057
Distinct Read Pairs	21824290	17176560
One Read Pair	21615208	16849216
Two Read Pairs	207442	322257
NRF = Distinct/Total	0.9904	0.9810
PBC1 = OnePair/Distinct	0.9904	0.9809
PBC2 = OnePair/TwoPair	104.1988	52.2850

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	43649046	34353366
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	43649046	34353366
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	43649046	34353366
Paired(QC-failed)	0	0
Read1	21824523	17176683
Read1(QC-failed)	0	0
Read2	21824523	17176683
Read2(QC-failed)	0	0
Properly Paired	43649046	34353366
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	43649046	34353366
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	60980
Np	0
N optimal	60980
N conservative	60980
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.	0.2026
Phantom Peak	50
Corr. Phantom Peak	0.1998
Argmin. Corr.	1500
Min. Corr.	0.1803
NSC	1.1237
RSC	1.1450

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	0.1325

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	0.1400
AUC	0.4938
CHANCE divergence	0.4537
Elbow Point	0.0000
JS Distance	0.6685
Synthetic AUC	0.4987
Synthetic Elbow Point	0.0966
Synthetic JS Distance	0.3707