Untitled

No description

Report generated at 2021-10-14 16:53:52

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	202884688	219088414
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	115049293	201201418
Mapped(QC-failed)	0	0
% Mapped	56.7100	91.8400
Paired	202884688	219088414
Paired(QC-failed)	0	0
Read1	101442344	109544207
Read1(QC-failed)	0	0
Read2	101442344	109544207
Read2(QC-failed)	0	0
Properly Paired	110860492	195093802
Properly Paired(QC-failed)	0	0
% Properly Paired	54.6400	89.0500
With itself	111677756	198729534
With itself(QC-failed)	0	0
Singletons	3371537	2471884
Singletons(QC-failed)	0	0
% Singleton	1.6600	1.1300
Diff. Chroms	204553	1686556
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	49315201	84750175
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	28045968	4543899
Paired Opt. Dupes	10208	16720
% Dupes/100	0.5687	0.0536

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	49314711	84743747
Distinct Read Pairs	21269008	80200171
One Read Pair	7923864	75870816
Two Read Pairs	5850099	4124763
NRF = Distinct/Total	0.4313	0.9464
PBC1 = OnePair/Distinct	0.3726	0.9460
PBC2 = OnePair/TwoPair	1.3545	18.3940

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	42538466	160412552
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	42538466	160412552
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	42538466	160412552
Paired(QC-failed)	0	0
Read1	21269233	80206276
Read1(QC-failed)	0	0
Read2	21269233	80206276
Read2(QC-failed)	0	0
Properly Paired	42538466	160412552
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	42538466	160412552
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	39652
Np	0
N optimal	39652
N conservative	39652
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.	210
Corr. Est. Fragment Len.	0.2641
Phantom Peak	55
Corr. Phantom Peak	0.2448
Argmin. Corr.	1500
Min. Corr.	0.1465
NSC	1.8026
RSC	1.1960

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	0.4772

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	0.1443
AUC	0.4938
CHANCE divergence	0.1796
Elbow Point	0.0000
JS Distance	0.8288
Synthetic AUC	0.5003
Synthetic Elbow Point	0.4723
Synthetic JS Distance	0.5315