Untitled

No description

Pipeline version: v1.1.7

Report generated at 2019-10-23 05:02:41

Paired-end: False

Pipeline type: TF ChIP-Seq

Genome: hg19_klab.tsv

Peak caller: SPP

Alignment

Flagstat (raw BAM)

	rep1	rep2	ctl1
Total	30259635	105480002	57444550
Total(QC-failed)	0	0	0
Dupes	0	0	0
Dupes(QC-failed)	0	0	0
Mapped	27477490	82279341	34552286
Mapped(QC-failed)	0	0	0
% Mapped	90.8100	78.0000	60.1500
Paired	0	0	0
Paired(QC-failed)	0	0	0
Read1	0	0	0
Read1(QC-failed)	0	0	0
Read2	0	0	0
Read2(QC-failed)	0	0	0
Properly Paired	0	0	0
Properly Paired(QC-failed)	0	0	0
% Properly Paired	0.0000	0.0000	0.0000
With itself	0	0	0
With itself(QC-failed)	0	0	0
Singletons	0	0	0
Singletons(QC-failed)	0	0	0
% Singleton	0.0000	0.0000	0.0000
Diff. Chroms	0	0	0
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

Filtered out (samtools view -F 1804):

read unmapped (0x4)
not primary alignment (0x100)
read fails platform/vendor quality checks (0x200)
read is PCR or optical duplicate (0x400)

	rep1	rep2	ctl1
Unpaired Reads	21944641	56746292	22975627
Paired Reads	0	0	0
Unmapped Reads	0	0	0
Unpaired Dupes	7444848	14284011	206977
Paired Dupes	0	0	0
Paired Opt. Dupes	0	0	0
% Dupes/100	0.3393	0.2517	0.0090

Library complexity (filtered non-mito BAM)

	rep1	rep2	ctl1
Total Reads	21927446	56549710	22886568
Distinct Reads	14924471	45206270	22788081
One Read	10322775	36294421	22701124
Two Reads	3249462	7163006	83850
NRF = Distinct/Total	0.6806	0.7994	0.9957
PBC1 = OneRead/Distinct	0.6917	0.8029	0.9962
PBC2 = OneRead/TwoReads	3.1768	5.0669	270.7349

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	rep2	ctl1
Total	14499793	42462281	22768650
Total(QC-failed)	0	0	0
Dupes	0	0	0
Dupes(QC-failed)	0	0	0
Mapped	14499793	42462281	22768650
Mapped(QC-failed)	0	0	0
% Mapped	100.0000	100.0000	100.0000
Paired	0	0	0
Paired(QC-failed)	0	0	0
Read1	0	0	0
Read1(QC-failed)	0	0	0
Read2	0	0	0
Read2(QC-failed)	0	0	0
Properly Paired	0	0	0
Properly Paired(QC-failed)	0	0	0
% Properly Paired	0.0000	0.0000	0.0000
With itself	0	0	0
With itself(QC-failed)	0	0	0
Singletons	0	0	0
Singletons(QC-failed)	0	0	0
% Singleton	0.0000	0.0000	0.0000
Diff. Chroms	0	0	0
Diff. Chroms (QC-failed)	0	0	0

Peak calling

IDR (Irreproducible Discovery Rate) plots

Reproducibility QC and peak detection statistics

The number of peaks is capped at 300K for peak-caller SPP

	overlap	IDR
Nt	78098	44835
N1	71693	53391
N2	82823	37715
Np	103230	56667
N optimal	103230	56667
N conservative	78098	44835
Optimal Set	ppr	ppr
Conservative Set	rep1-rep2	rep1-rep2
Rescue Ratio	1.3218	1.2639
Self Consistency Ratio	1.1552	1.4156
Reproducibility	pass	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'

IDR (Irreproducible Discovery Rate) peaks

N1: Replicate 1 self-consistent IDR 0.05 peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent IDR 0.05 peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Nt: True Replicate consistent IDR 0.05 peaks (comparing true replicates Rep1 vs Rep2 )
Np: Pooled-pseudoreplicate consistent IDR 0.05 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	rep2
Reads	15000000	15000000
Est. Fragment Len.	115	120
Corr. Est. Fragment Len.	0.3540	0.2034
Phantom Peak	40	35
Corr. Phantom Peak	0.2166	0.1913
Argmin. Corr.	1500	1500
Min. Corr.	0.0956	0.1523
NSC	3.7028	1.3355
RSC	2.1361	1.3095

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-rep2	rep1-pr	rep2-pr	ppr
Fraction of Reads in Peak	0.1258	0.2599	0.0881	0.1371

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)

Fraction of reads in IDR peaks

	rep1-rep2	rep1-pr	rep2-pr	ppr
Fraction of Reads in Peak	0.1080	0.2428	0.0673	0.1180

ppr: IDR peaks comparing pooled pseudo replicates
rep1-pr: IDR peaks comparing pseudoreplicates from replicate 1
rep2-pr: IDR peaks comparing pseudoreplicates from replicate 2
repi-repj: IDR peaks comparing true replicates (rep i vs. rep j)

Other quality metrics

Fingerprint and Jensen-Shannon distance

	rep1	rep2
% genome enriched	0.1649	0.2233
AUC	0.4845	0.4910
CHANCE divergence	0.3106	0.1685
Elbow Point	0.0000	0.0000
JS Distance	0.7225	0.6186
Synthetic AUC	0.5162	0.5096
Synthetic Elbow Point	0.2870	0.1316
Synthetic JS Distance	0.3990	0.3380