QC Report

	general
Report generated at	2021-03-29 16:53:14
Title	max_sk
Description	chipseq of max_sk
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}, 'ctl4': {'paired_end': False}}
Peak caller	macs2

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2	ctl1	ctl2	ctl3	ctl4
Total Reads	25567970	27566553	21297488	33377133	29140141	31388493
Total Reads (QC-failed)	0	0	0	0	0	0
Duplicate Reads	0	0	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0	0	0
Mapped Reads	23706705	25583851	20739516	31521519	26650521	30389001
Mapped Reads (QC-failed)	0	0	0	0	0	0
% Mapped Reads	92.7	92.80000000000001	97.39999999999999	94.39999999999999	91.5	96.8
Paired Reads	0	0	0	0	0	0
Paired Reads (QC-failed)	0	0	0	0	0	0
Read1	0	0	0	0	0	0
Read1 (QC-failed)	0	0	0	0	0	0
Read2	0	0	0	0	0	0
Read2 (QC-failed)	0	0	0	0	0	0
Properly Paired Reads	0	0	0	0	0	0
Properly Paired Reads (QC-failed)	0	0	0	0	0	0
% Properly Paired Reads	0.0	0.0	0.0	0.0	0.0	0.0
With itself	0	0	0	0	0	0
With itself (QC-failed)	0	0	0	0	0	0
Singletons	0	0	0	0	0	0
Singletons (QC-failed)	0	0	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0	0	0
Diff. Chroms (QC-failed)	0	0	0	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1	ctl2	ctl3	ctl4
Unpaired Reads	20250618	22193386	17693290	24547084	19534522	25076254
Paired Reads	0	0	0	0	0	0
Unmapped Reads	0	0	0	0	0	0
Unpaired Duplicate Reads	682357	1389794	595624	513327	371642	514421
Paired Duplicate Reads	0	0	0	0	0	0
Paired Optical Duplicate Reads	0	0	0	0	0	0
% Duplicate Reads	3.3695999999999997	6.2622	3.3664	2.0912	1.9025	2.0514

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	ctl4
Total Reads	20250618	22193386	17693290	24547084	19534522	25076254
Total Reads (QC-failed)	0	0	0	0	0	0
Duplicate Reads	0	0	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0	0	0
Mapped Reads	20250618	22193386	17693290	24547084	19534522	25076254
Mapped Reads (QC-failed)	0	0	0	0	0	0
% Mapped Reads	100.0	100.0	100.0	100.0	100.0	100.0
Paired Reads	0	0	0	0	0	0
Paired Reads (QC-failed)	0	0	0	0	0	0
Read1	0	0	0	0	0	0
Read1 (QC-failed)	0	0	0	0	0	0
Read2	0	0	0	0	0	0
Read2 (QC-failed)	0	0	0	0	0	0
Properly Paired Reads	0	0	0	0	0	0
Properly Paired Reads (QC-failed)	0	0	0	0	0	0
% Properly Paired Reads	0.0	0.0	0.0	0.0	0.0	0.0
With itself	0	0	0	0	0	0
With itself (QC-failed)	0	0	0	0	0	0
Singletons	0	0	0	0	0	0
Singletons (QC-failed)	0	0	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0	0	0
Diff. Chroms (QC-failed)	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	ctl1	ctl2	ctl3	ctl4
Total Fragments	20229518	22161652	17198856	24243200	19333997	24729367
Distinct Fragments	19555482	20788858	17073203	24009839	19139394	24537431
Positions with Two Read	592081	1185343	113955	201213	172224	178029
NRF = Distinct/Total	0.966681	0.938055	0.992694	0.990374	0.989935	0.992239
PBC1 = OneRead/Distinct	0.967885	0.938815	0.993141	0.991338	0.990702	0.992574
PBC2 = OneRead/TwoRead	31.967694	16.465178	148.796464	118.291855	110.097495	136.80479

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	62942	23190
N1	47458	18090
N2	66789	25962
Np	67818	27523
N optimal	67818	27523
N conservative	62942	23190
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.077468145276604	1.186847779215179
Self Consistency Ratio	1.4073285852754014	1.4351575456053067
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	139224	213745

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	90.0	85.0	88.0	88.0
25 percentile	90.0	85.0	277.0	183.0
50 percentile (median)	123.0	107.0	395.0	269.0
75 percentile	203.0	181.0	574.0	407.0
Max size	2980.0	2354.0	3221.0	3221.0
Mean	180.38892001379074	162.59901284240567	461.70442902299897	332.8542864726179

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	15000000	15000000
Estimated Fragment Length	90	85
Cross-correlation at Estimated Fragment Length	0.218483846936243	0.213987584136038
Phantom Peak	55	55
Cross-correlation at Phantom Peak	0.2125842	0.209574
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.1615382	0.1587911
NSC (Normalized Strand Cross-correlation coeff.)	1.352521	1.347604
RSC (Relative Strand Cross-correlation coeff.)	1.115576	1.086911

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	0.21875511441493345	0.2064937852003627
Synthetic AUC	0.488960623605279	0.4894695011664095
X-intercept	0.1775650484039299	0.18306522234618106
Synthetic X-intercept	1.7707558851283847e-69	1.8565937660044864e-76
Elbow Point	0.6818836146399395	0.6783507875385372
Synthetic Elbow Point	0.5080337330664835	0.5027662534221174
JS Distance	0.16960580272870676	0.17173607739513408
Synthetic JS Distance	0.3493264895037891	0.36928631504263665
% Genome Enriched	30.628631294410255	30.521666806620203
Diff. Enrichment	15.37233097355512	17.583455363555224
CHANCE Divergence	0.13495821894913748	0.15522592014651768

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	0.17178804123409963	0.20572791371267096	0.1859061288894986	0.22048749118318403	0.18605743291389923	0.22114804834197	0.1885458073182728	0.18294428584070438	0.18310379011367542

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	0.15790979569222546	0.13228658009350627	0.15300680121546123	0.16180829687981368

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	0.10717855459631	0.09076735337163537	0.10681511149312682	0.11617231022784749

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