QC Report

	general
Report generated at	2021-03-29 04:02:05
Title	max_a549_1
Description	chipseq of max_a549_1
Pipeline version	v1.3.6
Pipeline type	tf
Genome	hg38
Aligner	bowtie2
Sequencing endedness	{'rep1': {'paired_end': False}, 'rep2': {'paired_end': False}, 'ctl1': {'paired_end': False}, 'ctl2': {'paired_end': False}, 'ctl3': {'paired_end': False}}
Peak caller	macs2

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2	ctl1	ctl2	ctl3
Total Reads	37084542	27209605	21838401	28259579	46716344
Total Reads (QC-failed)	0	0	0	0	0
Duplicate Reads	0	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0	0
Mapped Reads	34166379	26274009	21043939	25670739	43648353
Mapped Reads (QC-failed)	0	0	0	0	0
% Mapped Reads	92.10000000000001	96.6	96.39999999999999	90.8	93.4
Paired Reads	0	0	0	0	0
Paired Reads (QC-failed)	0	0	0	0	0
Read1	0	0	0	0	0
Read1 (QC-failed)	0	0	0	0	0
Read2	0	0	0	0	0
Read2 (QC-failed)	0	0	0	0	0
Properly Paired Reads	0	0	0	0	0
Properly Paired Reads (QC-failed)	0	0	0	0	0
% Properly Paired Reads	0.0	0.0	0.0	0.0	0.0
With itself	0	0	0	0	0
With itself (QC-failed)	0	0	0	0	0
Singletons	0	0	0	0	0
Singletons (QC-failed)	0	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0	0
Diff. Chroms (QC-failed)	0	0	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1	ctl2	ctl3
Unpaired Reads	28921256	22741927	17304118	19909098	35669427
Paired Reads	0	0	0	0	0
Unmapped Reads	0	0	0	0	0
Unpaired Duplicate Reads	2784874	897327	246513	314955	848702
Paired Duplicate Reads	0	0	0	0	0
Paired Optical Duplicate Reads	0	0	0	0	0
% Duplicate Reads	9.6292	3.9457	1.4246	1.582	2.3794

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	ctl3
Total Reads	28921256	22741927	17304118	19909098	35669427
Total Reads (QC-failed)	0	0	0	0	0
Duplicate Reads	0	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0	0
Mapped Reads	28921256	22741927	17304118	19909098	35669427
Mapped Reads (QC-failed)	0	0	0	0	0
% Mapped Reads	100.0	100.0	100.0	100.0	100.0
Paired Reads	0	0	0	0	0
Paired Reads (QC-failed)	0	0	0	0	0
Read1	0	0	0	0	0
Read1 (QC-failed)	0	0	0	0	0
Read2	0	0	0	0	0
Read2 (QC-failed)	0	0	0	0	0
Properly Paired Reads	0	0	0	0	0
Properly Paired Reads (QC-failed)	0	0	0	0	0
% Properly Paired Reads	0.0	0.0	0.0	0.0	0.0
With itself	0	0	0	0	0
With itself (QC-failed)	0	0	0	0	0
Singletons	0	0	0	0	0
Singletons (QC-failed)	0	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0	0
Diff. Chroms (QC-failed)	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	ctl1	ctl2	ctl3
Total Fragments	28863996	22678528	17128808	19737029	35287964
Distinct Fragments	26117606	21824509	17034087	19571133	34797271
Positions with Two Read	2232214	700754	87294	143591	446150
NRF = Distinct/Total	0.904851	0.962342	0.99447	0.991595	0.986095
PBC1 = OneRead/Distinct	0.905617	0.964931	0.994731	0.992397	0.986846
PBC2 = OneRead/TwoRead	10.596003	30.052122	194.106468	135.261486	76.968614

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	54270	26896
N1	48059	23205
N2	47963	21316
Np	56173	29146
N optimal	56173	29146
N conservative	54270	26896
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.035065413672379	1.0836555621653778
Self Consistency Ratio	1.0020015428559514	1.0886188778382435
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	139694	109157

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	105.0	105.0	105.0	105.0
25 percentile	105.0	116.0	383.0	237.0
50 percentile (median)	142.0	171.0	598.0	375.0
75 percentile	270.0	309.0	922.0	655.0
Max size	4840.0	4005.0	5922.0	5922.0
Mean	257.50229072114763	271.256218107863	707.7546490084403	510.9441546650526

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	15000000	15000000
Estimated Fragment Length	105	105
Cross-correlation at Estimated Fragment Length	0.214504688895308	0.234636345553612
Phantom Peak	55	55
Cross-correlation at Phantom Peak	0.2096057	0.2246216
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.1604932	0.1693512
NSC (Normalized Strand Cross-correlation coeff.)	1.336535	1.385502
RSC (Relative Strand Cross-correlation coeff.)	1.099751	1.181195

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	0.2234858499820152	0.20427682927413424
Synthetic AUC	0.4907726691999949	0.4896072140648285
X-intercept	0.1425221125701764	0.1855516546440396
Synthetic X-intercept	6.34800774705566e-100	1.5719283698558214e-78
Elbow Point	0.6648945954159402	0.6710065418019545
Synthetic Elbow Point	0.49471232818735295	0.508667883547616
JS Distance	0.17272645146933913	0.16774652016034133
Synthetic JS Distance	0.3653624442797773	0.37442685502212125
% Genome Enriched	22.882311543321443	22.700172741958703
Diff. Enrichment	17.744947400840083	17.621522845264437
CHANCE Divergence	0.15115877608304695	0.15067633966938668

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	0.2015069815778402	0.19450818745482737	0.1966329539768259	0.18817445908719788	0.19688398041910765	0.18788355920250555	0.20035050879462846	0.1923517141336082	0.19240917061593302

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	0.18030412489296294	0.1701391875926827	0.16535854679333023	0.18147286821255285

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	0.15058957943028792	0.13946634959422233	0.12829282232767697	0.1543243280229172

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