QC Report

	general
Report generated at	2021-08-28 13:24:33
Title	cebp-1_RW12290_youngadult_1_4
Description	gevirl
Pipeline version	v1.3.6
Pipeline type	tf
Genome	WS245chr
Aligner	bwa
Sequencing endedness	{'rep1': {'paired_end': True}, 'rep2': {'paired_end': True}, 'ctl1': {'paired_end': True}}
Peak caller	spp

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2	ctl1
Total Reads	14398900	16886908	16282238
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	14341913	16782740	16262911
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.6	99.4	99.9
Paired Reads	14398900	16886908	16282238
Paired Reads (QC-failed)	0	0	0
Read1	7199450	8443454	8141119
Read1 (QC-failed)	0	0	0
Read2	7199450	8443454	8141119
Read2 (QC-failed)	0	0	0
Properly Paired Reads	14300760	16732936	16146240
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.3	99.1	99.2
With itself	14333372	16773162	16253516
With itself (QC-failed)	0	0	0
Singletons	8541	9578	9395
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	3667	4575	19348
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	6550683	7636705	7372701
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	755913	967525	836691
Paired Optical Duplicate Reads	43039	55124	51054
% Duplicate Reads	11.5395	12.6694	11.3485

Filtered out (samtools view -F 1804):

read unmapped (0x4)
mate unmapped (0x8, for paired-end)
not primary alignment (0x100)
read fails platform/vendor quality checks (0x200)
read is PCR or optical duplicate (0x400)

SAMstat (filtered/deduped BAM)

	rep1	rep2	ctl1
Total Reads	11589540	13338360	13072020
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	11589540	13338360	13072020
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	11589540	13338360	13072020
Paired Reads (QC-failed)	0	0	0
Read1	5794770	6669180	6536010
Read1 (QC-failed)	0	0	0
Read2	5794770	6669180	6536010
Read2 (QC-failed)	0	0	0
Properly Paired Reads	11589540	13338360	13072020
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	11589540	13338360	13072020
With itself (QC-failed)	0	0	0
Singletons	0	0	0
Singletons (QC-failed)	0	0	0
% Singleton	0.0	0.0	0.0
Diff. Chroms	0	0	0
Diff. Chroms (QC-failed)	0	0	0

Filtered and duplicates removed

Sequence quality metrics (filtered/deduped BAM)

Open chromatin assays are known to have significant GC bias. Please take this into consideration as necessary.

Library complexity quality metrics

Library complexity (filtered non-mito BAM)

	rep1	rep2	ctl1
Total Fragments	6519109	7598061	7314532
Distinct Fragments	5769356	6638911	6487025
Positions with Two Read	614218	771067	685244
NRF = Distinct/Total	0.884991	0.873764	0.886868
PBC1 = OneRead/Distinct	0.882367	0.870454	0.883931
PBC2 = OneRead/TwoRead	8.288087	7.494637	8.367945

Mitochondrial reads are filtered out by default. The non-redundant fraction (NRF) is the fraction of non-redundant mapped reads in a dataset; it is the ratio between the number of positions in the genome that uniquely mapped reads map to and the total number of uniquely mappable reads. The NRF should be > 0.8. The PBC1 is the ratio of genomic locations with EXACTLY one read pair over the genomic locations with AT LEAST one read pair. PBC1 is the primary measure, and the PBC1 should be close to 1. Provisionally 0-0.5 is severe bottlenecking, 0.5-0.8 is moderate bottlenecking, 0.8-0.9 is mild bottlenecking, and 0.9-1.0 is no bottlenecking. The PBC2 is the ratio of genomic locations with EXACTLY one read pair over the genomic locations with EXACTLY two read pairs. The PBC2 should be significantly greater than 1. See more details at the ENCODE portal standard for ChIP-Seq pipeline

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

Replication quality metrics

IDR (Irreproducible Discovery Rate) plots

Reproducibility QC and peak detection statistics

	overlap	idr
Nt	33150	1546
N1	26350	1488
N2	30807	797
Np	33983	1969
N optimal	33983	1969
N conservative	33150	1546
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0251282051282051	1.2736093143596379
Self Consistency Ratio	1.169146110056926	1.8670012547051442
Reproducibility Test	pass	pass

Reproducibility QC

N1: Replicate 1 self-consistent peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Ni: Replicate i self-consistent peaks (comparing two pseudoreplicates generated by subsampling RepX reads)
Nt: True Replicate consistent peaks (comparing true replicates Rep1 vs Rep2)
Np: Pooled-pseudoreplicate consistent 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'

Number of raw peaks

	rep1	rep2
Number of peaks	61264	69495

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	72.0	70.0	76.0	76.0
25 percentile	290.0	280.0	304.0	304.0
50 percentile (median)	290.0	280.0	304.0	304.0
75 percentile	290.0	280.0	304.0	304.0
Max size	564.0	516.0	891.0	891.0
Mean	289.4123792112823	279.78224332685807	283.81665820213306	302.83012094282435

Enrichment / Signal-to-noise ratio

Strand cross-correlation measures (trimmed/filtered SE BAM)

	rep1	rep2
Number of Subsampled Reads	6129680	7140369
Estimated Fragment Length	165	160
Cross-correlation at Estimated Fragment Length	0.66232503457035	0.689714014065659
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6593129	0.6886018
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6521714	0.6833298
NSC (Normalized Strand Cross-correlation coeff.)	1.015569	1.009343
RSC (Relative Strand Cross-correlation coeff.)	1.421781	1.210968

Performed on subsampled (15000000) reads mapped from FASTQs that are trimmed to 50. Such FASTQ trimming and subsampling reads are for cross-corrleation analysis only. Untrimmed FASTQs are used for all the other analyses.

NOTE1: For SE datasets, reads from replicates are randomly subsampled to 15000000.
NOTE2: For PE datasets, the first end (R1) of each read-pair is selected and trimmed to 50 the reads are then randomly subsampled to 15000000.

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

Jensen-Shannon distance (filtered/deduped BAM)

	rep1	rep2
AUC	0.3998146180644177	0.40863761422666217
Synthetic AUC	0.4981276370428844	0.49825300784757004
X-intercept	0.01944088012787637	0.019207397991255395
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5482260346551349	0.5249277103384693
Synthetic Elbow Point	0.49846921585574633	0.5027907331291773
JS Distance	0.06740606535415548	0.04770313454834444
Synthetic JS Distance	0.15239431290070707	0.13866003219810524
% Genome Enriched	40.280058829516136	42.299379975214976
Diff. Enrichment	10.189378067336346	8.911868490448938
CHANCE Divergence	0.08665778193396388	0.07574069012026832

Peak enrichment

Fraction of reads in peaks (FRiP)

FRiP for spp raw peaks

	rep1	rep2	rep1-pr1	rep2-pr1	rep1-pr2	rep2-pr2	pooled	pooled-pr1	pooled-pr2
Fraction of Reads in Peaks	0.32714810078743417	0.34161186232790236	0.36024932827359846	0.3757614879190545	0.361356360994483	0.36780983569194414	0.5245608334436515	0.34357992450226454	0.32761829115168145

FRiP for overlap peaks

	rep1_vs_rep2	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.1852570011914361	0.16326920654314148	0.1680883556899049	0.18953473818492533

FRiP for IDR peaks

	rep1_vs_rep2	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.019763036597547325	0.0231393998381299	0.01117311273649834	0.023254265301128455

For spp raw peaks:

repX: Peak from true replicate X
repX-prY: Peak from Yth pseudoreplicates from replicate X
pooled: Peak from pooled true replicates (pool of rep1, rep2, ...)
pooled-pr1: Peak from 1st pooled pseudo replicate (pool of rep1-pr1, rep2-pr1, ...)
pooled-pr2: Peak from 2nd pooled pseudo replicate (pool of rep1-pr2, rep2-pr2, ...)

For overlap/IDR peaks:

repX_vs_repY: Comparing two peaks from true replicates X and Y
repX-pr1_vs_repX-pr2: Comparing two peaks from both pseudoreplicates from replicate X
pooled-pr1_vs_pooled-pr2: Comparing two peaks from 1st and 2nd pooled pseudo replicates