Table 1 Relations defined in STQL for comparing different intervals

I₁ coincides with I₂

I₁.chr = I₂.chr and I₁.chrstart = I₂.chrstart and I₁.chrend = I₂.chrend

From the tracks of two replicated experiments where each interval stores the average signal of a genomic bin, find out the bins with values in both experiments

I₁ overlaps with I₂

I₁.chr = I₂.chr and I₁.chrstart ≤ I₂.chrend and I₁.chrend ≥ I₂.chrstart

From a track of intervals that represent a type of signal, find out those that overlap the promoters defined as intervals in another track

I₁ contains I₂

I₁.chr = I₂.chr and I₁.chrstart ≤ I₂.chrstart and I₁.chrend ≥ I₂.chrend

From a track of intervals that represent transcription factor binding sites, find out those that contain single nucleotide variants defined as intervals in another track

I₁ is within I₂

I₁.chr = I₂.chr and I₁.chrstart ≥ I₂.chrstart and I₁.chrend ≤ I₂.chrend

From a track of intervals that represent genes, find out those that are contained by haplotype blocks defined as intervals in another track

I₁ is adjacent to I₂

I₁.chr = I₂.chr and (I₁.chrend + 1 = I₂.chrstart or I₁.chrstart − 1 = I2.chrend)

From a track of intervals that represent different sequence elements, find out the flanking exons of an intron

I₁ is prefix of I₂

I₁.chr = I₂.chr and I₁.chrstart = I₂.chrstart and I₁.chrend ≤ I₂.chrend

From a track of intervals that represent genes and their sub-elements, find out the first exon of each gene on the positive strand

I₁ is suffix of I₂

I₁.chr = I₂.chr and I₁.chrstart ≥ I₂.chrstart and I₁.chrend = I₂.chrend

From a track of intervals that represent genes and their sub-elements, find out the first exon of each gene on the negative strand

I₁ precedes I₂

I₁.chr = I₂.chr and I₁.chrend < I₂.chrstart

Ordering any type of intervals on the same chromosome

I₁ follows I₂

I₁.chr = I₂.chr and I₁.chrstart > I₂.chrend

Ordering any type of intervals on the same chromosome

I₁ is upstream of I₂

I₁.chr = I₂.chr and ((I₂.strand = ‘ + ’ and I₁.strand = ‘ + ’ and I₁ precedes I₂) or (I₂.strand = ‘ + ’ and I₁.strand = ‘.’ and I₁ precedes I₂) or (I₂.strand = ‘ −’ and I₁.strand = ‘ −’ and I₁ follows I₂) or (I₂.strand = ‘ −’ and I₁.strand = ‘.’ and I₁ follows I₂))

From a track of intervals that represent transcripts, define their promoter regions

I₁ is downstream of I₂

I₁.chr = I₂.chr and ((I₂.strand = ‘ + ’ and I₁.strand = ‘ + ’ and I₁ follows I₂) or (I₂.strand = ‘ + ’ and I₁.strand = ‘.’ and I₁ follows I₂) or (I₂.strand = ‘ −’ and I₁.strand = ‘ −’ and I₁ precedes I₂) or (I₂.strand = ‘ −’ and I₁.strand = ‘.’ and I₁ precedes I₂))

From a track of intervals that represent sequence motifs, find out their downstream sequence elements defined as intervals in another track