Use cases¶

1) Quick telomere overview (fast mode)¶

Use fast mode to quickly summarize unmapped reads.

telomerehunter2 -ibt sample.bam -o results/ -p SampleID --fast_mode

2) Non-human / custom repeats¶

Provide custom telomeric repeats and (optionally) the repeat context.

telomerehunter2 \
  -ibt sample.bam \
  -o results/ \
  -p SampleID \
  --repeats TTTAGGG TTAAGGG \
  --repeatsContext TTAAGGG

3) Run without cytoband file¶

A cytoband file improves subtelomeric classification. If you do not provide -b, analysis can still run, but subtelomeric/junction assignments may be limited.

telomerehunter2 -ibt sample.bam -o results/ -p SampleID

4) Single-cell: rerun postprocessing with different filtering¶

If you want to adjust --min-reads-per-barcode without repeating the expensive filtering step, rerun with --noFiltering.

telomerehunter2-sc \
  -ibt sc_sample.bam \
  -o results/ \
  -p SampleID \
  -b telomerehunter2/cytoband_files/cytoband.txt \
  --min-reads-per-barcode 5000 \
  --noFiltering

5) Containers¶

If you run via Docker/Apptainer, the command-line interface is identical; ensure your input and output paths are mounted into the container.