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Track Conversion

TrackNado automatically converts common formats to UCSC-compatible indexed files if the conversion flag is set.

Supported Formats

  • BED to BigBed: Automatically sorts and converts BED files.
  • GTF/GFF to BigGenePred: Converts gene annotations to the bigGenePred format, allowing for codon and amino acid display when zoomed in.

Usage

CLI

tracknado create -i data/*.gtf -o gene_hub --convert --chrom-sizes hg38.chrom.sizes

API

builder.with_convert_files().with_chrom_sizes("hg38.chrom.sizes")

Backend Requirements

TrackNado attempts to find UCSC tools (bedToBigBed, gtfToGenePred, etc.) in your $PATH. If not found, it will automatically pull and run them via Docker or Apptainer.