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Genomic coordinates

All genomic coordinates splicekit operates with are 0-based, left+right inclusive. E.g. the range 100-103 includes coordinates 100, 101, 102 and 103; the first coordinate is 0.

More specifically:

  • Feature-specific: all feature coordinates (junctions, anchors, exons) are given in numeric sort order regardless of strand — feature_start is always < feature_stop. Example: chr1+_100_102 represents a junction spanning coordinates [100, 101, 102]; chr1-_100_102 represents a junction spanning coordinates [102, 101, 100].
  • Junction-specific: junction coordinates cover/overlap 1 nucleotide of each adjoining exon.
    • chr1+_100_200 — a junction on chromosome 1 (+ strand) from [100..200]. 100 is the last nucleotide of the upstream exon, 200 is the first nucleotide of the downstream exon.
    • chr1-_100_200 — a junction on chromosome 1 (- strand) from [100..200]. 200 is the last nucleotide of the upstream exon, 100 is the first nucleotide of the downstream exon.

Important

RefSeq and Ensembl GTF files are 1-indexed. When splicekit reads files from RefSeq/Ensembl, it performs coordinate -= 1 on every coordinate to keep them consistent with splicekit's internal 0-indexed structures.