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FAQ

Where do I get a cytoband file?

TelomereHunter2 ships cytoband files under telomerehunter2/cytoband_files/. Use the one matching your reference build (e.g. hg19 vs GRCh38) when available.

Can I run without -b?

Yes. The tool can run without a cytoband file, but subtelomeric/junction classification may be reduced.

The run is slow / uses too much RAM. What can I do?

  • Reduce cores via -c (if available in your version)
  • Use --fast_mode for a quick overview
  • Ensure input BAM/CRAM is indexed and stored on fast storage

How do I change the barcode tag for single-cell?

Use --barcodeTag to match the tag used in your BAM (default is typically CB).

Plot export fails (kaleido/chrome)

Static image export via kaleido may require chrome/chromium. If you only need TSV outputs, disable plotting (option name depends on your run mode; see --help).

TelomereHunter2

TelomereHunter2 is a Python tool for estimating telomere content and analyzing telomeric variant repeats (TVRs) from genome sequencing data.

What you can do

  • Bulk telomere content estimation from BAM/CRAM inputs
  • Tumor vs control comparison (log2 ratio)
  • Single-cell BAM analysis (barcode-aware)
  • Generate static/interactive reports

Where to start

  • Read the Intro to understand the concepts.
  • Follow the Quickstart to run your first analysis.
  • Check Use cases for common workflows.
  • See FAQ if you run into issues.