QC Report

	general
Report generated at	2024-02-13 13:33:30
Title	nsy-7_RW12353_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	29901224	31783000	34387604
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	17532873	21991993	20159222
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	58.599999999999994	69.19999999999999	58.599999999999994
Paired Reads	29901224	31783000	34387604
Paired Reads (QC-failed)	0	0	0
Read1	14950612	15891500	17193802
Read1 (QC-failed)	0	0	0
Read2	14950612	15891500	17193802
Read2 (QC-failed)	0	0	0
Properly Paired Reads	17475920	21923394	19905916
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	58.4	69.0	57.9
With itself	17519612	21974082	20109516
With itself (QC-failed)	0	0	0
Singletons	13261	17911	49706
Singletons (QC-failed)	0	0	0
% Singleton	0.0	0.1	0.1
Diff. Chroms	8839	11423	94519
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	7943944	9997756	8810080
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	915314	1090848	868103
Paired Optical Duplicate Reads	472434	538627	574302
% Duplicate Reads	11.5222	10.9109	9.8535

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	14057260	17813816	15883954
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	14057260	17813816	15883954
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	14057260	17813816	15883954
Paired Reads (QC-failed)	0	0	0
Read1	7028630	8906908	7941977
Read1 (QC-failed)	0	0	0
Read2	7028630	8906908	7941977
Read2 (QC-failed)	0	0	0
Properly Paired Reads	14057260	17813816	15883954
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	14057260	17813816	15883954
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	7892475	9937111	8752386
Distinct Fragments	6916201	8812682	7835374
Positions with Two Read	676534	823916	655892
NRF = Distinct/Total	0.876303	0.886845	0.895227
PBC1 = OneRead/Distinct	0.886893	0.89309	0.90418
PBC2 = OneRead/TwoRead	9.066694	9.552571	10.801454

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	72164	1836
N1	57057	1228
N2	64398	1078
Np	72579	1809
N optimal	72579	1836
N conservative	72164	1836
Optimal Set	pooled-pr1_vs_pooled-pr2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.005750789867524	1.0149253731343284
Self Consistency Ratio	1.1286608128713391	1.1391465677179964
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	109931	114380

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	68.0	68.0	70.0	70.0
25 percentile	270.0	270.0	280.0	280.0
50 percentile (median)	270.0	270.0	280.0	280.0
75 percentile	270.0	270.0	280.0	280.0
Max size	482.0	372.0	620.0	620.0
Mean	269.8759312659759	269.9011890190593	269.80991285403053	279.7345375384064

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	7341147	9282802
Estimated Fragment Length	180	180
Cross-correlation at Estimated Fragment Length	0.693521804731544	0.740506043966811
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6891615	0.7368163
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.685463	0.7336581
NSC (Normalized Strand Cross-correlation coeff.)	1.011757	1.009334
RSC (Relative Strand Cross-correlation coeff.)	2.178964	2.168315

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	0.40425353477137876	0.4138025486788334
Synthetic AUC	0.4982870675465028	0.49848215487771486
X-intercept	0.018785489746020657	0.01847811985429869
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5563434958335413	0.5380769422683499
Synthetic Elbow Point	0.4987360968473683	0.5002190140242989
JS Distance	0.047011229304952516	0.04671335038723433
Synthetic JS Distance	0.14924994477960754	0.13655327276227908
% Genome Enriched	27.19385260216556	26.809041464996756
Diff. Enrichment	6.575098630802245	4.962319957181238
CHANCE Divergence	0.058362490733434066	0.04432972314900132

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	0.4312358169372979	0.4334254378736145	0.4574128955429436	0.4601315069157557	0.4550812889567384	0.45761290000974525	0.4110909214361009	0.43343732731207446	0.4343414072370823

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	0.2906087325071799	0.24822255546244432	0.2647699965015918	0.29188813706823075

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	0.01950975862879559	0.01614845282793375	0.012721137346428189	0.01921234162285578

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