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File conversion

UCSC track hubs work best with indexed formats such as bigWig and bigBed. TrackNado can convert BED files to bigBed and GTF/GFF files to bigGenePred while it builds the hub.

Convert during a build

Provide --convert and a chromosome-sizes file for the target assembly:

tracknado create \
  -i annotations/genes.gtf \
  -i peaks/regions.bed \
  --output my_hub \
  --genome-name hg38 \
  --convert \
  --chrom-sizes hg38.chrom.sizes

The chromosome sizes must match the genome assembly and the chromosome names in your input. A mismatch is a common cause of conversion or display failures.

Converted files are written under my_hub/converted before staging. The original source files are not changed.

The same configuration in Python is:

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

Tool requirements

TrackNado looks for the UCSC conversion programs, including bedToBigBed and gtfToGenePred, on PATH. If they are unavailable, it can run them through Docker or Apptainer. Make sure one of these routes is available before running a large conversion job.

Formats that need preparation

  • bigWig and bigBed can be included directly.
  • BED is converted to bigBed with --convert.
  • GTF/GFF is converted to bigGenePred with --convert.
  • BAM needs a same-named .bai index next to it, for example sample.bam.bai. TrackNado stops early with a clear error if it cannot find the index.

For repeatable production hubs, consider converting and validating data in your analysis workflow, then give TrackNado the finished UCSC-ready files.