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Given a list of gene identifiers and a gene annotation in .gff3 format, uses bedtools closest to find neighbouring, and potentially overlapping, genes for each gene on the list.


  • latest bedtools version

Usage: bash -k=<check k nearest neighbours, default: 2> -o=<OUTPUT_PREFIX (default: tandem)> --min-overlap=<minimum number of overlapping bases, default: 0 - no overlap required> --max-distance=<maximum distance between neighbouring genes to be reported, default=100bp> <list_of_gene-ids> <annotation_in_gff3-format> will generate 5 output files:

  • OUTPUT_PREFIX.k.FF.tsv Neighbouring/overlapping genes in forward/forward orientation
  • OUTPUT_PREFIX.k.RF.tsv Neighbouring/overlapping genes in reverse/forward orientation
  • OUTPUT_PREFIX.k.FR.tsv Neighbouring/overlapping genes in forward/reverse orientation
  • OUTPUT_PREFIX.k.RR.tsv Neighbouring/overlapping genes in reverse/reverse orientation
  • OUTPUT_PREFIX.k.full.tsv Overlapping genes with one gene completely containing the other