ChipAlignmentEnrichmentQualityMetric

TF, Histone

subsampled_reads

Number of reads subsampled from the sample for calculation of all cross-correlation metrics

estimated_fragment_len

Fragment length/strandshift. This is the estimated fragment length/strand shift for each dataset as estimated by strand shift cross-correlation analysis

corr_estimated_fragment_len

Value of correlation function at estimated fragment length.

phantom_peak

Strand shift value at which the phantom (false) peak in cross-correlation is observed. This is typically the read length.

corr_phantom_peak

Value of cross-correlation function at strand shift corresponding to phantom_peak (which is typically the read length)

argmin_corr

Strand shift corresponding to the minimum value of cross-correlation (min_corr)

min_corr

Minimum cross-correlation over a sufficiently wide range of strand shifts (typically -100 bp to ~3 times the expected size of DNA fragments based on sonication and size selection protocols).

NSC

Normalized strand cross-correlation = FRAGLEN_CC / MIN_CC. Ratio of strand cross-correlation at estimated fragment length to the minimum cross-correlation over all shifts.

RSC

Relative cross-correlation coefficient. Ratio of strand cross-correlation at fragment length and at read length

auc

The “area under the curve”, with a maximum value of 0.5. Lower values generally indicate higher and more focal enrichment.

syn_auc

The expected area under the curve of a perfectly behaved input sample having the same mean sequencing depth of a given sample. This is useful to put the observed AUC into perspective.

x_intercept

The point (on the X-axis) at which the curve is 0. This is approximately the percentage of the genome that was not sequenced in a particular sample.

syn_x_intercept

The expected X-intercept of a perfectly behaved input sample having the same mean sequencing depth of a given sample. This is useful to put the observed X-intercept into perspective.

elbow_pt

The elbow point attempts to measure the position at which the line turns upward. In practice, this is the point at which the plotted line is furthest from the line from the lower-left to the upper-right corner of the graph (equivalent to a perfect input sample with infinite coverage). The point returned is the position on the X-axis of this elbow point and higher values indicate more enrichment.

syn_elbow_pt

The expected elbow point of a perfectly behaved input sample having the same mean sequencing depth of a given sample. This is useful to put the observed elbow point into perspective.

jsd

The Jensen-Shannon distance between the replicate and the control.

syn_jsd

The Jensen-Shannon distance between a given sample and a perfect input sample with the same coverage depth (i.e., the plot generated from the Poisson probability mass function with lambda equal to the mean coverage in the sample).

pct_genome_enrich

The approximate percentage of the genome enriched in signal (e.g., bound by a transcription factor or having a certain histone modification).

diff_enrich

The differential enrichment between a given sample and that indicated by --JSDsample at the elbow point.

ch_div

The CHANCE divergence between the replicate and the control.

ChipAlignmentQualityMetric

TF, Histone

total_reads

Number of total reads passing QC"

total_reads_qc_failed

Number of total reads failing QC

duplicate_reads

Number of reads with duplicates passing QC

duplicate_reads_qc_failed

Number of reads with duplicates failing QC

mapped_reads

Number of mapped reads passing QC

mapped_reads_qc_failed

Number of mapped reads failing QC

pct_mapped_reads

Percent of mapped reads passing QC

paired_reads

Number of paired reads passing QC

paired_reads_qc_failed

Number of paired reads failing QC

read1

Number of read1 reads passing QC

read1_qc_failed

Number of read1 reads failing QC

read2

Number of read2 reads passing QC

read2_qc_failed

Number of read2 reads failing QC

properly_paired_reads

Number of properly paired reads passing QC

properly_paired_reads_qc_failed

Number of properly paired reads failing QC

pct_properly_paired_reads

Percent of properly paired reads passing QC

with_itself

Number of reads with both itself & mate mapped passing QC

with_itself_qc_failed

Number of reads with both itself & mate mapped failing QC

singletons

Number of singletons (unpaired reads) passing QC

singletons_qc_failed

Number of singletons (unpaired reads) failing QC

pct_singletons

Percent of singletons (unpaired reads) passing QC

diff_chroms

Number of reads with mate mapped to different chromosomes passing QC

diff_chroms_qc_failed

Number of reads with mate mapped to different chromosomes failing QC

usable_fragments

Usable fragments, based on the mapped_reads value.

ChipLibraryQualityMetric

TF, Histone

unpaired_reads

Number of unpaired reads before filtering

paired_reads

Number of paired reads before duplicate filtering

unmapped_reads

Number of unmapped reads before duplicate filtering

unpaired_duplicate_reads

Number of unpaired duplicates before duplicate filtering

paired_duplicate_reads

Number of paired duplicates before duplicate filtering

paired_optical_duplicate_reads

Number of paired optical duplicates before duplicate filtering

pct_duplicate_reads

Percent of paired duplicates before duplicate filtering

total_fragments

Number of fragments before duplicate filtering

distinct_fragments

Number of distinct fragments

positions_with_one_read

Number of locations to which exactly one read (pair) maps

NRF

Non redundant fraction (indicates library complexity). Number of distinct unique mapping reads (i.e. after removing duplicates) / Total number of reads

PBC1

PCR Bottlenecking coefficient 1 = M1/M_DISTINCT where M1: number of genomic locations where exactly one read maps uniquely, M_DISTINCT: number of distinct genomic locations to which some read maps uniquely

PBC2

PCR Bottlenecking coefficient 2 (indicates library complexity) = M1/M2 where M1: number of genomic locations where only one read maps uniquely and M2: number of genomic locations where 2 reads map uniquely

ChipPeakEnrichmentQualityMetric

TF, Histone

frip

Fraction of reads in the peak file

min_size

Smallest peak width

25_pct

25th percentile of peak widths

50_pct

50th percentile of peak widths

75_pct

75th percentile of peak widths

max_size

Largest peak width

mean

Mean peak width

ChipReplicationQualityMetric

TF, Histone

reproducible_peaks

Number of peaks called from one replicate or pooled replicates passing reproducibility test by comparing self-pseudoreplicates or pooled pseudo-replicates.

idr_cutoff

Irreproducible Discovery Rate (IDR) threshold used to define reproducible peaks

rescue_ratio

max(Np,Nt) / min (Np,Nt); Np: Pooled-pseudoreplicate consistent peaks (comparing two pseudoreplicates generated by subsampling pooled reads from Rep1 and Rep2); Nt: True Replicate consistent peaks (comparing true replicates Rep1 vs Rep2)

self_consistency_ratio

max(N1,N2) / min (N1,N2); N1: Replicate 1 self-consistent peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads); N2: same as N1 for Rep2

reproducibility

Reproducibility test result for this experiment (pass/fail)

ChipSeqFilterQualityMetric

Deprecated

NSC

Normalized strand cross-correlation = FRAGLEN_CC / MIN_CC. Ratio of strand cross-correlation at estimated fragment length to the minimum cross-correlation over all shifts.

RSC

Relative cross correlation coefficient. Ratio of strand cross-correlation at fragment length and at read length

PBC1

PCR Bottlenecking coefficient 1 = M1/M_DISTINCT where M1: number of genomic locations where exactly one read maps uniquely, M_DISTINCT: number of distinct genomic locations to which some read maps uniquely

PBC2

PCR Bottlenecking coefficient 2 (indicates library complexity) = M1/M2 where M1: number of genomic locations where only one read maps uniquely and M2: number of genomic locations where 2 reads map uniquely

fragment length

Fragment length/strandshift. This is the estimated fragment length/strand shift for each dataset as estimated by strand cross-correlation analysis

NRF

Non redundant fraction (indicates library complexity). Number of distinct unique mapping reads (i.e. after removing duplicates) / Total number of reads

ComplexityXcorrQualityMetric

Deprecated

sample size

Total reads sampled (pairs if applicable)

paired-end

Reads are paired-ended

read length

Read length

fragment length

Fragment length/strandshift. This is the estimated fragment length/strand shift for each dataset as estimated by strand cross-correlation analysis

NRF

Non redundant fraction (indicates library complexity). Distinct Locations Mapped / Sampled Reads

PBC1

PCR Bottlenecking coefficient 1 = Single-read Locations / Distinct Locations

PBC2

PCR Bottlenecking coefficient 2 (indicates library complexity) = Single-read Locations / Multi-read Locations

NSC

Normalized strand cross-correlation = FRAGLEN_CC / MIN_CC. Ratio of strand cross-correlation at estimated fragment length to the minimum cross-correlation over all shifts.

RSC

Relative cross correlation coefficient. Ratio of strand cross-correlation at fragment length and at read length

cross_correlation_plot

Cross-correlation plot

HistoneChipSeqQualityMetric

Deprecated

nreads

# of starting reads in the pool (if replicated) or experiment (if unreplicated)

nreads_in_peaks

# of reads that fall within peaks.

npeak_overlap

# peaks overlapping with true replicate or pooled pseudoreplicate peaks

Fp

Fraction reads in replicated/stable narrowPeaks (FRiP) from pooled pseudoreplicates

Ft

Fraction reads in replicated/stable narrowPeaks (FRiP) from true replicates

F1

Fraction reads in replicated/stable narrowPeaks (FRiP) from replicate 1 self-pseudoreplicates that pass internal pseudoreplication, when self-pseudoreplication is done on unreplicated experiments.

F2

Fraction reads in replicated/stable narrowPeaks (FRiP) from replicate 2 self-pseudoreplicates

frip

Best fraction reads in peaks (FRiP) from peaks

IDRQualityMetric

Deprecated

Fp

Fraction reads in IDR peaks (FRiP) from pooled pseudoreplicates

Ft

Fraction reads in IDR peaks (FRiP) from true replicates

F1

Fraction reads in peaks (FRiP) from replicate 1 self-pseudoreplicates that pass the internal pseudoreplication IDR threshold, when self-pseudoreplication is done on unreplicated experiments.

F2

Fraction reads in peaks (FRiP) from replicate 2 self-pseudoreplicates

Np

Number of peaks from pooled pseudoreplicates

Nt

Number of peaks from true replicates

N1

Number of peaks from replicate 1 self-pseudoreplicates that pass the internal pseudoreplication IDR threshold, when self-pseudoreplication is done on unreplicated experiments.

N2

Number of peaks from replicate 2 self-pseudoreplicates

IDR_cutoff

IDR cutoff threshold for this experiment

self_consistency_ratio

IDR self-consistency ratio for this experiment

rescue_ratio

IDR rescue ratio for this experiment

reproducibility_test

IDR reproducibility test result for this experiment

N_optimal

Number of peaks in the IDR optimal set

N_conservative

Number of peaks in the IDR conservative set

IDR_plot_true

IDR dispersion plot for true replicates

IDR_plot_rep1_pr

IDR dispersion plot for replicate 1 pseudo-replicates

IDR_plot_rep2_pr

IDR dispersion plot for replicate 2 pseudo-replicates

IDR_plot_pool_pr

IDR dispersion plot for pool pseudo-replicates

IDR_parameters_true

IDR run parameters for true replicates

IDR_parameters_rep1_pr

IDR run parameters for replicate 1 pseudo-replicates

IDR_parameters_rep2_pr

IDR run parameters for replicate 2 pseudo-replicates

IDR_parameters_pool_pr

IDR run parameters for pool pseudo-replicates

frip

Fraction reads in IDR peaks (FRiP) from optimal peaks

IdrSummaryQualityMetric

Deprecated

Final parameter values (mu, sigma, rho, and mix)

IDR: Final parameter values (mu, sigma, rho, and mix)

IDR cutoff

IDR: IDR cutoff

Initial parameter values (mu, sigma, rho, and mix)

IDR: Initial parameter values (mu, sigma, rho, and mix)

Number of peaks passing IDR cutoff

IDR: Number of peaks passing IDR cutoff

Number of reported peaks

IDR: Number of reported peaks

Percent peaks passing IDR cutoff

IDR: Percent peaks passing IDR cutoff

Percent reported peaks

IDR: Percent reported peaks