QC Report

	general
Report generated at	2021-09-14 02:32:33
Title	cebp-2_OP331_youngadult_1_1
Description	mkudron
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	12856630	21307752	14875582
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	12409005	20859835	14380443
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	96.5	97.89999999999999	96.7
Paired Reads	12856630	21307752	14875582
Paired Reads (QC-failed)	0	0	0
Read1	6428315	10653876	7437791
Read1 (QC-failed)	0	0	0
Read2	6428315	10653876	7437791
Read2 (QC-failed)	0	0	0
Properly Paired Reads	12368936	20795542	14321246
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	96.2	97.6	96.3
With itself	12401992	20840890	14373000
With itself (QC-failed)	0	0	0
Singletons	7013	18945	7443
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	3957	6235	23840
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	5641702	9477902	6586813
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	615230	1170527	851151
Paired Optical Duplicate Reads	46925	112182	71976
% Duplicate Reads	10.905	12.3501	12.922

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	10052944	16614750	11471324
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	10052944	16614750	11471324
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	10052944	16614750	11471324
Paired Reads (QC-failed)	0	0	0
Read1	5026472	8307375	5735662
Read1 (QC-failed)	0	0	0
Read2	5026472	8307375	5735662
Read2 (QC-failed)	0	0	0
Properly Paired Reads	10052944	16614750	11471324
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	10052944	16614750	11471324
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	5606764	9420955	6516977
Distinct Fragments	4996691	8265157	5678617
Positions with Two Read	506677	930978	677847
NRF = Distinct/Total	0.89119	0.877316	0.871358
PBC1 = OneRead/Distinct	0.888741	0.874521	0.867194
PBC2 = OneRead/TwoRead	8.764483	7.763935	7.264858

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	76747	1062
N1	35227	254
N2	49165	386
Np	86840	1419
N optimal	86840	1419
N conservative	76747	1062
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.1315100264505453	1.3361581920903955
Self Consistency Ratio	1.3956624180316235	1.5196850393700787
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	113614	140650

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	79.0	61.0	68.0	68.0
25 percentile	264.0	244.0	270.0	270.0
50 percentile (median)	264.0	244.0	270.0	270.0
75 percentile	264.0	244.0	270.0	270.0
Max size	264.0	244.0	270.0	270.0
Mean	263.9931698558276	243.99137575542125	268.1592670894996	269.9699216950714

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	5279616	8856360
Estimated Fragment Length	145	150
Cross-correlation at Estimated Fragment Length	0.629712828235883	0.7357339426301
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.629977	0.7353622
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6256922	0.7308015
NSC (Normalized Strand Cross-correlation coeff.)	1.006426	1.006749
RSC (Relative Strand Cross-correlation coeff.)	0.9383494	1.081509

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	0.39901586904732533	0.40735717289007456
Synthetic AUC	0.49798585582455857	0.498431739314623
X-intercept	0.01916179854664913	0.018804548058173953
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5405539178802872	0.5381629341641236
Synthetic Elbow Point	0.49823927550844704	0.4985728914590785
JS Distance	0.03811030802785582	0.02963461491364819
Synthetic JS Distance	0.150218252787191	0.1409310869330498
% Genome Enriched	43.47299365930278	44.51540667679209
Diff. Enrichment	9.214955322951667	8.032438423048971
CHANCE Divergence	0.07841207951146062	0.06836794947286133

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	0.49269706466085955	0.5348555349914985	0.4155861208418151	0.43175474421766874	0.41860155592232484	0.42786372685279367	0.5265674639884499	0.5379544599578456	0.5379892643127872

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	0.33040805852954513	0.1817338284188194	0.21895153402849876	0.3666791361862784

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	0.009503633872505062	0.0032187586044446284	0.004021607306760559	0.011989300612193915

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