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Report generated at 2021-10-10 02:01:21

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	98301252	116616760
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	97129919	115340967
Mapped(QC-failed)	0	0
% Mapped	98.8100	98.9100
Paired	98301252	116616760
Paired(QC-failed)	0	0
Read1	49150626	58308380
Read1(QC-failed)	0	0
Read2	49150626	58308380
Read2(QC-failed)	0	0
Properly Paired	95620127	112618961
Properly Paired(QC-failed)	0	0
% Properly Paired	97.2700	96.5700
With itself	96513479	114670631
With itself(QC-failed)	0	0
Singletons	616440	670336
Singletons(QC-failed)	0	0
% Singleton	0.6300	0.5700
Diff. Chroms	411927	1356484
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	37864321	46805405
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2271877	2581950
Paired Opt. Dupes	42244	44282
% Dupes/100	0.0600	0.0552

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	37864150	46788318
Distinct Read Pairs	35592284	44207269
One Read Pair	33379042	41662261
Two Read Pairs	2156765	2510205
NRF = Distinct/Total	0.9400	0.9448
PBC1 = OnePair/Distinct	0.9378	0.9424
PBC2 = OnePair/TwoPair	15.4764	16.5972

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	71184888	88446910
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	71184888	88446910
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	71184888	88446910
Paired(QC-failed)	0	0
Read1	35592444	44223455
Read1(QC-failed)	0	0
Read2	35592444	44223455
Read2(QC-failed)	0	0
Properly Paired	71184888	88446910
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	71184888	88446910
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	180021
Np	0
N optimal	180021
N conservative	180021
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.	120
Corr. Est. Fragment Len.	0.1811
Phantom Peak	50
Corr. Phantom Peak	0.1921
Argmin. Corr.	1500
Min. Corr.	0.1768
NSC	1.0244
RSC	0.2804

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	0.1578

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	0.2114
AUC	0.4941
CHANCE divergence	0.2039
Elbow Point	0.0000
JS Distance	0.6001
Synthetic AUC	0.5007
Synthetic Elbow Point	0.2107
Synthetic JS Distance	0.3574