Untitled

No description

Report generated at 2021-02-10 03:19:19

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	93552906	193594802
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	78035817	187969057
Mapped(QC-failed)	0	0
% Mapped	83.4100	97.0900
Paired	93552906	193594802
Paired(QC-failed)	0	0
Read1	46776453	96797401
Read1(QC-failed)	0	0
Read2	46776453	96797401
Read2(QC-failed)	0	0
Properly Paired	75417395	184287983
Properly Paired(QC-failed)	0	0
% Properly Paired	80.6100	95.1900
With itself	76858238	185784698
With itself(QC-failed)	0	0
Singletons	1177579	2184359
Singletons(QC-failed)	0	0
% Singleton	1.2600	1.1300
Diff. Chroms	100300	610670
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	33944715	78211821
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1625695	539110
Paired Opt. Dupes	5994	19807
% Dupes/100	0.0479	0.0069

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	33863251	77646644
Distinct Read Pairs	32243121	77172156
One Read Pair	30689427	76701136
Two Read Pairs	1489688	467668
NRF = Distinct/Total	0.9522	0.9939
PBC1 = OnePair/Distinct	0.9518	0.9939
PBC2 = OnePair/TwoPair	20.6012	164.0077

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	64638040	155345422
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	64638040	155345422
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	64638040	155345422
Paired(QC-failed)	0	0
Read1	32319020	77672711
Read1(QC-failed)	0	0
Read2	32319020	77672711
Read2(QC-failed)	0	0
Properly Paired	64638040	155345422
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	64638040	155345422
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	94080
Np	0
N optimal	94080
N conservative	94080
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.	135
Corr. Est. Fragment Len.	0.1793
Phantom Peak	50
Corr. Phantom Peak	0.1912
Argmin. Corr.	1500
Min. Corr.	0.1722
NSC	1.0410
RSC	0.3732

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	0.1487

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	0.2798
AUC	0.4949
CHANCE divergence	0.1048
Elbow Point	0.0000
JS Distance	0.6070
Synthetic AUC	0.5001
Synthetic Elbow Point	0.1647
Synthetic JS Distance	0.2849