QC Report

	general
Report generated at	2020-05-20 00:30:13
Title	tye7_nit_exo
Description	chip exo data for tye7 (nitrogen limited)
Pipeline version	v1.3.6
Pipeline type	tf
Genome	sacCer3
Aligner	bowtie2
Sequencing endedness	{'rep1': {'paired_end': False}, 'rep2': {'paired_end': False}, 'ctl1': {'paired_end': True}, 'ctl2': {'paired_end': True}}
Peak caller	macs2

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2	ctl1	ctl2
Total Reads	10326358	13242221	3555302	2475684
Total Reads (QC-failed)	0	0	0	0
Duplicate Reads	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0
Mapped Reads	9665976	11749039	1729789	2119384
Mapped Reads (QC-failed)	0	0	0	0
% Mapped Reads	93.60000000000001	88.7	48.699999999999996	85.6
Paired Reads	0	0	3555302	2475684
Paired Reads (QC-failed)	0	0	0	0
Read1	0	0	1777651	1237842
Read1 (QC-failed)	0	0	0	0
Read2	0	0	1777651	1237842
Read2 (QC-failed)	0	0	0	0
Properly Paired Reads	0	0	1624258	1980632
Properly Paired Reads (QC-failed)	0	0	0	0
% Properly Paired Reads	0.0	0.0	45.7	80.0
With itself	0	0	1628458	1982620
With itself (QC-failed)	0	0	0	0
Singletons	0	0	101331	136764
Singletons (QC-failed)	0	0	0	0
% Singleton	0.0	0.0	2.9000000000000004	5.5
Diff. Chroms	0	0	546	783
Diff. Chroms (QC-failed)	0	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1	ctl2
Unpaired Reads	7907712	9570977	0	0
Paired Reads	0	0	581306	779111
Unmapped Reads	0	0	0	0
Unpaired Duplicate Reads	7639498	9255148	0	0
Paired Duplicate Reads	0	0	551622	738554
Paired Optical Duplicate Reads	0	0	0	0
% Duplicate Reads	96.6082	96.7001	94.8936	94.7945

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	ctl2
Total Reads	7907712	9570977	1162612	1558222
Total Reads (QC-failed)	0	0	0	0
Duplicate Reads	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0
Mapped Reads	7907712	9570977	1162612	1558222
Mapped Reads (QC-failed)	0	0	0	0
% Mapped Reads	100.0	100.0	100.0	100.0
Paired Reads	0	0	1162612	1558222
Paired Reads (QC-failed)	0	0	0	0
Read1	0	0	581306	779111
Read1 (QC-failed)	0	0	0	0
Read2	0	0	581306	779111
Read2 (QC-failed)	0	0	0	0
Properly Paired Reads	0	0	1162612	1558222
Properly Paired Reads (QC-failed)	0	0	0	0
% Properly Paired Reads	0.0	0.0	100.0	100.0
With itself	0	0	1162612	1558222
With itself (QC-failed)	0	0	0	0
Singletons	0	0	0	0
Singletons (QC-failed)	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0
Diff. Chroms (QC-failed)	0	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	ctl2
Total Fragments	7850210	9456854	579915	776487
Distinct Fragments	378698	444100	29612	40375
Positions with Two Read	27221	32629	1244	1466
NRF = Distinct/Total	0.04824	0.046961	0.051063	0.051997
PBC1 = OneRead/Distinct	0.221517	0.222328	0.068722	0.065684
PBC2 = OneRead/TwoRead	3.081738	3.02602	1.635852	1.809004

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	1915	32
N1	4822	3508
N2	4450	3376
Np	3333	2599
N optimal	3333	2599
N conservative	1915	32
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.7404699738903395	81.21875
Self Consistency Ratio	1.0835955056179776	1.0390995260663507
Reproducibility Test	pass	borderline

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	5678	5234

Top 500000 raw peaks from macs2 with p-val threshold 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	150.0	150.0	150.0	150.0
25 percentile	154.0	158.0	185.0	180.0
50 percentile (median)	211.0	217.0	242.0	235.0
75 percentile	299.0	303.0	329.0	315.0
Max size	2975.0	4855.0	4803.0	4803.0
Mean	252.896090172596	257.90771876194117	282.69988457098884	272.6216621662166

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	7850210	9456854
Estimated Fragment Length	95	185
Cross-correlation at Estimated Fragment Length	0.386473665471152	0.421158442524564
Phantom Peak	70	70
Cross-correlation at Phantom Peak	0.3864968	0.422186
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.378503	0.4144173
NSC (Normalized Strand Cross-correlation coeff.)	1.021058	1.016266
RSC (Relative Strand Cross-correlation coeff.)	0.9971089	0.8677273

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	0.3652913139565758	0.3652913139565758
Synthetic AUC	0.4991779715745877	0.4991779715745877
X-intercept	0.043175796656728556	0.043175796656728556
Synthetic X-intercept	1e-323	1e-323
Elbow Point	0.5189768103854285	0.5189768103854285
Synthetic Elbow Point	0.5000976225608418	0.5000976225608418
JS Distance	0.2670066144843168	0.2670066144843168
Synthetic JS Distance	0.1932217686601569	0.1932217686601569
% Genome Enriched	49.857775066755465	49.857775066755465
Diff. Enrichment	14.643097344308275	14.643097344308275
CHANCE Divergence	0.12777932525852032	0.12777932525852032

Peak enrichment

Fraction of reads in peaks (FRiP)

FRiP for macs2 raw peaks

	rep1	rep2	rep1-pr1	rep2-pr1	rep1-pr2	rep2-pr2	pooled	pooled-pr1	pooled-pr2
Fraction of Reads in Peaks	0.3078031926301818	0.2719307548226268	0.3106648294727982	0.2744068578989524	0.3122946308616196	0.27375640687010394	0.20284908095795973	0.20209168993786147	0.20520636331514128

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	0.12085431578993139	0.2778679850758348	0.24591418410053645	0.180397397081669

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	0.013775518289729853	0.2202260274526943	0.19966519614455244	0.14962603888655493

For macs2 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