QC Report

	general
Report generated at	2021-08-31 19:22:51
Title	pes-1_RW12239_earlyembryonic_1_3
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	39771542	41175882	76333708
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	38696248	40549393	76225816
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	97.3	98.5	99.9
Paired Reads	39771542	41175882	76333708
Paired Reads (QC-failed)	0	0	0
Read1	19885771	20587941	38166854
Read1 (QC-failed)	0	0	0
Read2	19885771	20587941	38166854
Read2 (QC-failed)	0	0	0
Properly Paired Reads	38348034	40350336	75508548
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	96.39999999999999	98.0	98.9
With itself	38664398	40513320	76169872
With itself (QC-failed)	0	0	0
Singletons	31850	36073	55944
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	9172	11850	278570
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	17269565	18294027	34441575
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	2705453	2747422	3607037
Paired Optical Duplicate Reads	141483	165028	299347
% Duplicate Reads	15.665999999999999	15.0181	10.472900000000001

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	29128224	31093210	61669076
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	29128224	31093210	61669076
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	29128224	31093210	61669076
Paired Reads (QC-failed)	0	0	0
Read1	14564112	15546605	30834538
Read1 (QC-failed)	0	0	0
Read2	14564112	15546605	30834538
Read2 (QC-failed)	0	0	0
Properly Paired Reads	29128224	31093210	61669076
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	29128224	31093210	61669076
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	17130029	18182257	34216823
Distinct Fragments	14490666	15469377	30654794
Positions with Two Read	1973576	2061877	3036514
NRF = Distinct/Total	0.845922	0.850795	0.895898
PBC1 = OneRead/Distinct	0.842569	0.847156	0.892849
PBC2 = OneRead/TwoRead	6.18643	6.355844	9.013661

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	55072	1452
N1	55523	1041
N2	51193	1164
Np	56266	1793
N optimal	56266	1793
N conservative	55072	1452
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.02168070889018	1.2348484848484849
Self Consistency Ratio	1.0845818764284179	1.1181556195965419
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	101511	87078

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	65.0	81.0	82.0	82.0
25 percentile	260.0	324.0	275.0	330.0
50 percentile (median)	260.0	324.0	330.0	330.0
75 percentile	260.0	324.0	330.0	330.0
Max size	638.0	567.0	675.0	675.0
Mean	259.67083370275145	323.39569121936654	294.4339096486336	328.83727295347103

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	15000000	15000000
Estimated Fragment Length	135	160
Cross-correlation at Estimated Fragment Length	0.819151581522439	0.821454454351078
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.8189392	0.820523
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.8130334	0.8143176
NSC (Normalized Strand Cross-correlation coeff.)	1.007525	1.008764
RSC (Relative Strand Cross-correlation coeff.)	1.035957	1.150107

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	0.4151236891494966	0.4069749851919427
Synthetic AUC	0.4987959423086075	0.4988541431301935
X-intercept	0.018890011706204288	0.018357729596686245
Synthetic X-intercept	0.0	0.0
Elbow Point	0.52291114290574	0.5280898876404494
Synthetic Elbow Point	0.5012587967714501	0.5015491839368461
JS Distance	0.027544861465419245	0.028009531567023977
Synthetic JS Distance	0.135211401090865	0.14312870380258805
% Genome Enriched	32.36495342531542	34.39382872922649
Diff. Enrichment	3.9612194650370913	4.8056262848723215
CHANCE Divergence	0.03421403968218201	0.041125530553003976

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	0.38687528632023704	0.3840039031029604	0.4354923939063363	0.43188764158556536	0.4359899868938113	0.4307670665567863	0.3541412016193437	0.3895669973728292	0.3893713786148426

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	0.2553183804955558	0.2314280129128367	0.2556255851357901	0.26317508480452323

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	0.014505018263098817	0.015358299908707101	0.012894648059817562	0.019960119182814543

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