Untitled

No description

Report generated at 2021-10-21 12:07:17

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	131737656	216279744
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	117104629	212268741
Mapped(QC-failed)	0	0
% Mapped	88.8900	98.1500
Paired	131737656	216279744
Paired(QC-failed)	0	0
Read1	65868828	108139872
Read1(QC-failed)	0	0
Read2	65868828	108139872
Read2(QC-failed)	0	0
Properly Paired	115584153	208007441
Properly Paired(QC-failed)	0	0
% Properly Paired	87.7400	96.1800
With itself	116214236	210903306
With itself(QC-failed)	0	0
Singletons	890393	1365435
Singletons(QC-failed)	0	0
% Singleton	0.6800	0.6300
Diff. Chroms	274095	1643621
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	50548878	86702361
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	11402431	3631684
Paired Opt. Dupes	14354	20901
% Dupes/100	0.2256	0.0419

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	50541285	86645143
Distinct Read Pairs	39140504	83016384
One Read Pair	29926515	79488299
Two Read Pairs	7398010	3431092
NRF = Distinct/Total	0.7744	0.9581
PBC1 = OnePair/Distinct	0.7646	0.9575
PBC2 = OnePair/TwoPair	4.0452	23.1671

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	78292894	166141354
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	78292894	166141354
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	78292894	166141354
Paired(QC-failed)	0	0
Read1	39146447	83070677
Read1(QC-failed)	0	0
Read2	39146447	83070677
Read2(QC-failed)	0	0
Properly Paired	78292894	166141354
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	78292894	166141354
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	115941
Np	0
N optimal	115941
N conservative	115941
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.	185
Corr. Est. Fragment Len.	0.2007
Phantom Peak	50
Corr. Phantom Peak	0.1996
Argmin. Corr.	1500
Min. Corr.	0.1748
NSC	1.1481
RSC	1.0430

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	0.4152

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	0.1850
AUC	0.4944
CHANCE divergence	0.1246
Elbow Point	0.0000
JS Distance	0.7803
Synthetic AUC	0.5070
Synthetic Elbow Point	0.3586
Synthetic JS Distance	0.4453