Untitled

No description

Report generated at 2021-10-21 20:20:18

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	178934438	215916580
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	176020472	212163850
Mapped(QC-failed)	0	0
% Mapped	98.3700	98.2600
Paired	178934438	215916580
Paired(QC-failed)	0	0
Read1	89467219	107958290
Read1(QC-failed)	0	0
Read2	89467219	107958290
Read2(QC-failed)	0	0
Properly Paired	172512204	203494730
Properly Paired(QC-failed)	0	0
% Properly Paired	96.4100	94.2500
With itself	174835039	210124486
With itself(QC-failed)	0	0
Singletons	1185433	2039364
Singletons(QC-failed)	0	0
% Singleton	0.6600	0.9400
Diff. Chroms	1529578	4820338
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	72844852	84863940
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4630436	4207317
Paired Opt. Dupes	30515	26763
% Dupes/100	0.0636	0.0496

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	72841082	84737544
Distinct Read Pairs	68210904	80538942
One Read Pair	63820486	76496172
Two Read Pairs	4162221	3894193
NRF = Distinct/Total	0.9364	0.9505
PBC1 = OnePair/Distinct	0.9356	0.9498
PBC2 = OnePair/TwoPair	15.3333	19.6437

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	136428832	161313246
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	136428832	161313246
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	136428832	161313246
Paired(QC-failed)	0	0
Read1	68214416	80656623
Read1(QC-failed)	0	0
Read2	68214416	80656623
Read2(QC-failed)	0	0
Properly Paired	136428832	161313246
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	136428832	161313246
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	144778
Np	0
N optimal	144778
N conservative	144778
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.	155
Corr. Est. Fragment Len.	0.1884
Phantom Peak	50
Corr. Phantom Peak	0.1910
Argmin. Corr.	1500
Min. Corr.	0.1851
NSC	1.0174
RSC	0.5482

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	0.5203

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	0.1771
AUC	0.4957
CHANCE divergence	0.1106
Elbow Point	0.0000
JS Distance	0.7894
Synthetic AUC	0.5069
Synthetic Elbow Point	0.3636
Synthetic JS Distance	0.4588