QC Report

	general
Report generated at	2019-11-22 21:26:40
Title	AWRI1631--MSS11
Description	chipseq of yeast AWRI1631 for tf MSS11
Pipeline version	v1.3.3
Pipeline type	tf
Genome	AWRI1631
Paired-end per replicate	[True, True, True]
Aligner	bowtie2
Peak caller	spp
Control paired-end per replicate	[True, True, True, True]

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2	rep3	ctl1	ctl2	ctl3	ctl4
Total Reads	5540762	5891144	5104418	5917546	6601090	11652572	8804978
Total Reads (QC-failed)	0	0	0	0	0	0	0
Duplicate Reads	0	0	0	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0	0	0	0
Mapped Reads	4562352	4995381	4552001	4977004	5788309	9693515	6321027
Mapped Reads (QC-failed)	0	0	0	0	0	0	0
% Mapped Reads	82.3	84.8	89.2	84.1	87.7	83.2	71.8
Paired Reads	5540762	5891144	5104418	5917546	6601090	11652572	8804978
Paired Reads (QC-failed)	0	0	0	0	0	0	0
Read1	2770381	2945572	2552209	2958773	3300545	5826286	4402489
Read1 (QC-failed)	0	0	0	0	0	0	0
Read2	2770381	2945572	2552209	2958773	3300545	5826286	4402489
Read2 (QC-failed)	0	0	0	0	0	0	0
Properly Paired Reads	3850814	4150126	3814730	3717114	4357276	7216522	3826466
Properly Paired Reads (QC-failed)	0	0	0	0	0	0	0
% Properly Paired Reads	69.5	70.39999999999999	74.7	62.8	66.0	61.9	43.5
With itself	4505348	4862862	4463226	4894834	5693772	9527698	5338574
With itself (QC-failed)	0	0	0	0	0	0	0
Singletons	57004	132519	88775	82170	94537	165817	982453
Singletons (QC-failed)	0	0	0	0	0	0	0
% Singleton	1.0	2.1999999999999997	1.7000000000000002	1.4000000000000001	1.4000000000000001	1.4000000000000001	11.200000000000001
Diff. Chroms	1998	3203	2608	2445	2633	5103	2765
Diff. Chroms (QC-failed)	0	0	0	0	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	rep3	ctl1	ctl2	ctl3	ctl4
Unpaired Reads	0	0	0	0	0	0	0
Paired Reads	1626704	1349428	1227743	1618488	1908814	3134719	1665993
Unmapped Reads	0	0	0	0	0	0	0
Unpaired Duplicate Reads	0	0	0	0	0	0	0
Paired Duplicate Reads	16880	22119	16113	4666	7580	17416	5903
Paired Optical Duplicate Reads	561	393	280	658	501	1171	1570
% Duplicate Reads	1.0377	1.6391	1.3124	0.2883	0.39709999999999995	0.5556	0.3543

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	rep3	ctl1	ctl2	ctl3	ctl4
Total Reads	3219648	2654618	2423260	3227644	3802468	6234606	3320180
Total Reads (QC-failed)	0	0	0	0	0	0	0
Duplicate Reads	0	0	0	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0	0	0	0
Mapped Reads	3219648	2654618	2423260	3227644	3802468	6234606	3320180
Mapped Reads (QC-failed)	0	0	0	0	0	0	0
% Mapped Reads	100.0	100.0	100.0	100.0	100.0	100.0	100.0
Paired Reads	3219648	2654618	2423260	3227644	3802468	6234606	3320180
Paired Reads (QC-failed)	0	0	0	0	0	0	0
Read1	1609824	1327309	1211630	1613822	1901234	3117303	1660090
Read1 (QC-failed)	0	0	0	0	0	0	0
Read2	1609824	1327309	1211630	1613822	1901234	3117303	1660090
Read2 (QC-failed)	0	0	0	0	0	0	0
Properly Paired Reads	3219648	2654618	2423260	3227644	3802468	6234606	3320180
Properly Paired Reads (QC-failed)	0	0	0	0	0	0	0
% Properly Paired Reads	100.0	100.0	100.0	100.0	100.0	100.0	100.0
With itself	3219648	2654618	2423260	3227644	3802468	6234606	3320180
With itself (QC-failed)	0	0	0	0	0	0	0
Singletons	0	0	0	0	0	0	0
Singletons (QC-failed)	0	0	0	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0	0	0	0
Diff. Chroms (QC-failed)	0	0	0	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	rep3	ctl1	ctl2	ctl3	ctl4
Total Fragments	1624122	1344556	1223410	1571325	1852755	3044551	1629062
Distinct Fragments	1607335	1322596	1207399	1567386	1846120	3029617	1623881
Positions with Two Read	16264	20896	15374	3865	6528	14432	5101
NRF = Distinct/Total	0.989664	0.983667	0.986913	0.997493	0.996419	0.995095	0.99682
PBC1 = OneRead/Distinct	0.989722	0.983814	0.987012	0.997511	0.996436	0.995157	0.996835
PBC2 = OneRead/TwoRead	97.812039	62.269765	77.51509	404.523674	281.792279	208.906943	317.337973

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	2553	745
N1	3085	790
N2	1845	724
N3	1486	581
Np	2867	801
N optimal	2867	801
N conservative	2553	745
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep2_vs_rep3
Rescue Ratio	1.1229925577751665	1.0751677852348993
Self Consistency Ratio	2.076043068640646	1.359724612736661
Reproducibility Test	borderline	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	rep3
Number of peaks	7061	5516	5245

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	rep3	idr_opt	overlap_opt
Min size	118.0	95.0	85.0	104.0	104.0
25 percentile	470.0	380.0	340.0	331.0	416.0
50 percentile (median)	470.0	380.0	340.0	394.0	416.0
75 percentile	470.0	380.0	340.0	417.0	416.0
Max size	1690.0	1507.0	721.0	2077.0	2077.0
Mean	461.12207902563375	374.8651196519217	334.6655862726406	421.1972534332085	414.3906522497384

Enrichment / Signal-to-noise ratio

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

	rep1	rep2	rep3
Number of Subsampled Reads	2085785	1614866	1507444
Estimated Fragment Length	135	165	140
Cross-correlation at Estimated Fragment Length	0.867480791726332	0.819721399829387	0.811978482351318
Phantom Peak	50	55	55
Cross-correlation at Phantom Peak	0.8654684	0.8084903	0.8044345
Argmin of Cross-correlation	1500	1500	1500
Minimum of Cross-correlation	0.8447561	0.7720954	0.7747418
NSC (Normalized Strand Cross-correlation coeff.)	1.026901	1.061684	1.048063
RSC (Relative Strand Cross-correlation coeff.)	1.097158	1.308589	1.25407

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

Peak enrichment

Fraction of reads in peaks (FRiP)

FRiP for spp raw peaks

	rep1	rep2	rep3	rep1-pr1	rep2-pr1	rep3-pr1	rep1-pr2	rep2-pr2	rep3-pr2	pooled	pooled-pr1	pooled-pr2
Fraction of Reads in Peaks	0.3836319995229292	0.36273881967198296	0.33551661810948885	0.3766386884528992	0.3473544236086521	0.3089680843161691	0.3627508348738744	0.33051409318711256	0.2998638198129792	0.2726787478580965	0.3116614972555682	0.3179693122912329

FRiP for overlap peaks

	rep1_vs_rep2	rep1_vs_rep3	rep2_vs_rep3	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	rep3-pr1_vs_rep3-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.20199888496884494	0.17580770460978368	0.1948938755961717	0.23622861878068657	0.23407661667328405	0.18310416546305391	0.2353441254658316

FRiP for IDR peaks

	rep1_vs_rep2	rep1_vs_rep3	rep2_vs_rep3	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	rep3-pr1_vs_rep3-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.11767423205422918	0.10959881294737733	0.13778661253968955	0.11044685630230386	0.1696918351340946	0.12977682956017927	0.14288825367947025

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