> NSC values range from a minimum of 1 to larger positive numbers. 1.1 is the critical threshold. Datasets with NSC values much less than 1.1 (< 1.05) tend to have low signal to noise or few peaks (this could be biological eg.a factor that truly binds only a few sites in a particular tissue type OR it could be due to poor quality). RSC values range from 0 to larger positive values. 1 is the critical threshold. RSC values significantly lower than 1 (< 0.8) tend to have low signal to noise. The low scores can be due to failed and poor quality ChIP, low read sequence quality and hence lots of mismappings, shallow sequencing depth (significantly below saturation) or a combination of these. Like the NSC, datasets with few binding sites (< 200) which is biologically justifiable also show low RSC scores.
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col. abbreviation description
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1 Filename tagAlign/BAM filename
2 numReads effective sequencing depth i.e. total number of mapped reads in input file
3 estFragLen comma separated strand cross-correlation peak(s) in decreasing order of correlation.
4 corr_estFragLen comma separated strand cross-correlation value(s) in decreasing order (COL2 follows the same order)
needs to keep best SignalValue per interval, see R code below
### IDR
chrom string
Name of the chromosome for common peaks
chromStart int
The starting position of the feature in the chromosome or scaffold for common peaks, shifted based on offset. The first base in a chromosome is numbered 0.
chromEnd int
The ending position of the feature in the chromosome or scaffold for common peaks. The chromEnd base is not included in the display of the feature.
name string
Name given to a region (preferably unique) for common peaks. Use '.' if no name is assigned.
score int
Contains the scaled IDR value, min(int(log2(-125IDR), 1000). e.g. peaks with an IDR of 0 have a score of 1000, idr 0.05 have a score of int(-125log2(0.05)) = 540, and idr 1.0 has a score of 0.
strand [+-.] Use '.' if no strand is assigned.
signalValue float
Measurement of enrichment for the region for merged peaks. When a peak list is provided this is the value from the peak list.
p-value float
Merged peak p-value. When a peak list is provided this is the value from the peak list.
q-value float
Merged peak q-value. When a peak list is provided this is the value from the peak list.
summit int
Merged peak summit
localIDR float -log10(Local IDR value)
globalIDR float -log10(Global IDR value)
rep1_chromStart int
The starting position of the feature in the chromosome or scaffold for common replicate 1 peaks, shifted based on offset. The first base in a chromosome is numbered 0.
rep1_chromEnd int
The ending position of the feature in the chromosome or scaffold for common replicate 1 peaks. The chromEnd base is not included in the display of the feature.
rep1_signalValue float
Signal measure from replicate 1. Note that this is determined by the --rank option. e.g. if --rank is set to signal.value, this corresponds to the 7th column of the narrowPeak, whereas if it is set to p.value it corresponds to the 8th column.
